From 3a64a074c0729217f5b3a2329df74a98b6dfb753 Mon Sep 17 00:00:00 2001 From: lauthirteen <844125986@qq.com> Date: Thu, 27 Apr 2023 19:03:40 +0800 Subject: [PATCH 1/3] reading the MD_dump file of ABACUS3.2 --- dpdata/abacus/md.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py index 7532b7b2f..a8a798022 100644 --- a/dpdata/abacus/md.py +++ b/dpdata/abacus/md.py @@ -72,7 +72,7 @@ def get_coords_from_dump(dumplines, natoms): for iline in range(nlines): if "MDSTEP" in dumplines[iline]: # read in LATTICE_CONSTANT - celldm = float(dumplines[iline + 1].split(" ")[-1]) + celldm = float(dumplines[iline + 1].split(" ")[-2]) # read in LATTICE_VECTORS for ix in range(3): cells[iframe, ix] = ( @@ -98,7 +98,7 @@ def get_coords_from_dump(dumplines, natoms): [ float(i) for i in re.split("\s+", dumplines[iline + 11 + iat])[ - -6:-3 + 3:6 ] ] ) @@ -107,7 +107,7 @@ def get_coords_from_dump(dumplines, natoms): forces[iframe, iat] = np.array( [ float(i) - for i in re.split("\s+", dumplines[iline + 11 + iat])[-3:] + for i in re.split("\s+", dumplines[iline + 11 + iat])[6:9] ] ) else: @@ -116,7 +116,7 @@ def get_coords_from_dump(dumplines, natoms): [ float(i) for i in re.split("\s+", dumplines[iline + 7 + iat])[ - -6:-3 + 3:6 ] ] ) @@ -125,7 +125,7 @@ def get_coords_from_dump(dumplines, natoms): forces[iframe, iat] = np.array( [ float(i) - for i in re.split("\s+", dumplines[iline + 7 + iat])[-3:] + for i in re.split("\s+", dumplines[iline + 7 + iat])[6:9] ] ) iframe += 1 @@ -133,8 +133,8 @@ def get_coords_from_dump(dumplines, natoms): "iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump." % (iframe, nframes_dump) ) - cells *= bohr2ang - coords *= bohr2ang + #cells *= bohr2ang + #coords *= bohr2ang stresses *= kbar2evperang3 return coords, cells, forces, stresses From ba961a8e9cd4bc134cf52cba891c81ec53ff0fcb Mon Sep 17 00:00:00 2001 From: lauthirteen <844125986@qq.com> Date: Thu, 27 Apr 2023 19:15:15 +0800 Subject: [PATCH 2/3] reading the MD_dump file of ABACUS3.2 --- tests/abacus.md/OUT.abacus/MD_dump | 362 ++- tests/abacus.md/OUT.abacus/running_md.log | 3042 ++++++++------------- 2 files changed, 1416 insertions(+), 1988 deletions(-) diff --git a/tests/abacus.md/OUT.abacus/MD_dump b/tests/abacus.md/OUT.abacus/MD_dump index f35852368..c29983d00 100644 --- a/tests/abacus.md/OUT.abacus/MD_dump +++ b/tests/abacus.md/OUT.abacus/MD_dump @@ -1,80 +1,308 @@ MDSTEP: 0 -LATTICE_CONSTANT: 1.000000000000 +LATTICE_CONSTANT: 0.999999601891 Angstrom LATTICE_VECTORS - 28.000000000000 0.000000000000 0.000000000000 - 0.000000000000 28.000000000000 0.000000000000 - 0.000000000000 0.000000000000 28.000000000000 -VIRIAL (KBAR) - 0.342473709368 -0.250611694353 -0.053956446640 - -0.250611694353 0.199085269192 -0.098626841062 - -0.053956446640 -0.098626841062 0.476228570252 -INDEX LABEL POSITIONS FORCE (eV/Angstrom) - 0 H 15.953212941138 18.765586146743 8.395247471322 0.863308639441 -0.443254999104 -0.756985212833 - 1 H 13.771131204099 20.615493002741 7.611989524536 -0.200930881908 0.468126173231 -1.160958093908 - 2 O 14.513210882571 19.684192208442 8.958321352729 -0.662377757533 -0.024871174127 1.917943306741 + 8.783385481117 0.000000000000 0.000000000000 + 0.000000000000 8.783385481117 0.000000000000 + 0.000000000000 0.000000000000 8.783385481117 +VIRIAL (kbar) + 0.001159185406 0.000000030542 -0.000000001695 + 0.000000030542 0.001159187343 -0.000000000279 + -0.000000001695 -0.000000000279 0.001159187201 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Si 3.293768031087 1.097922677034 3.293768031103 -0.000000322619 0.000000834984 0.000002986129 0.000241770453 -0.000078797714 0.000166671325 + 1 Si 3.293768031103 1.097922677034 7.685458739241 -0.000000312188 0.000000861996 -0.000002993062 0.000099528289 -0.000189496581 0.000333008088 + 2 Si 3.293768031087 5.489613385172 3.293768031087 -0.000000334658 -0.000000835735 0.000002989300 -0.000612776533 0.000151435169 -0.000137606788 + 3 Si 3.293768031087 5.489613385172 7.685458739257 -0.000000311084 -0.000000862551 -0.000002980760 0.000594500675 -0.000660242566 0.000051097118 + 4 Si 7.685458739257 1.097922677034 3.293768031103 0.000000325494 0.000000821487 0.000002995598 0.000167538118 0.000444112053 -0.000328521382 + 5 Si 7.685458739241 1.097922677034 7.685458739241 0.000000309490 0.000000844350 -0.000002988208 -0.000000926534 -0.000082685173 0.000073795903 + 6 Si 7.685458739257 5.489613385156 3.293768031103 0.000000334197 -0.000000818321 0.000002958845 -0.000430128868 -0.000071564462 -0.000002537394 + 7 Si 7.685458739257 5.489613385172 7.685458739241 0.000000313855 -0.000000843907 -0.000002964683 0.000281580294 0.000280431960 -0.000478613860 + 8 Si 3.293768031087 3.293768031103 1.097922677050 -0.000000294392 -0.000000390064 -0.000002867759 0.000577365828 0.000143963081 -0.000018795477 + 9 Si 3.293768031087 3.293768031087 5.489613385156 -0.000000300179 -0.000000396605 0.000002867590 0.000048759956 -0.000200891714 0.000279139061 + 10 Si 3.293768031103 7.685458739241 1.097922677050 -0.000000348433 0.000000392509 -0.000002841024 -0.000047395785 0.000495230432 -0.000085668954 + 11 Si 3.293768031087 7.685458739257 5.489613385156 -0.000000337530 0.000000394876 0.000002840299 0.000176083713 -0.000375521726 -0.000289868737 + 12 Si 7.685458739257 3.293768031103 1.097922677050 0.000000301508 -0.000000409498 -0.000002835509 -0.000077589672 -0.000235035914 -0.000337413509 + 13 Si 7.685458739257 3.293768031103 5.489613385156 0.000000295478 -0.000000436526 0.000002833603 0.000076051771 0.000262938469 -0.000108826710 + 14 Si 7.685458739241 7.685458739241 1.097922677050 0.000000343733 0.000000404450 -0.000002809719 -0.000114939019 -0.000191399832 -0.000531467460 + 15 Si 7.685458739257 7.685458739241 5.489613385156 0.000000342384 0.000000437821 0.000002810715 -0.000006257033 -0.000168047400 0.000386630562 + 16 Si 1.097922677034 1.097922677050 1.097922677050 -0.000001915878 0.000000826791 -0.000002814933 -0.000046985501 0.000653775887 -0.000005211464 + 17 Si 1.097922677034 1.097922677034 5.489613385156 -0.000001921553 0.000000809370 0.000002813511 -0.000263723036 -0.000006416020 0.000203672528 + 18 Si 1.097922677034 5.489613385156 1.097922677050 -0.000001904579 -0.000000820777 -0.000002843048 0.000002408214 0.000074849682 -0.000285826559 + 19 Si 1.097922677019 5.489613385172 5.489613385156 -0.000001876639 -0.000000814347 0.000002845895 0.000203485499 0.000422981288 -0.000431370703 + 20 Si 5.489613385172 1.097922677034 1.097922677050 0.000001919264 0.000000869928 -0.000002827016 0.000058665567 -0.000245920097 -0.000064955631 + 21 Si 5.489613385172 1.097922677034 5.489613385156 0.000001917993 0.000000856396 0.000002828697 0.000211260340 0.000319412251 -0.000168369638 + 22 Si 5.489613385172 5.489613385172 1.097922677050 0.000001898859 -0.000000873795 -0.000002868949 -0.000167099120 0.000131603840 -0.000341025660 + 23 Si 5.489613385188 5.489613385172 5.489613385156 0.000001880055 -0.000000851582 0.000002864117 0.000310439222 0.000185081091 0.000014143359 + 24 Si 1.097922677034 3.293768031103 3.293768031103 -0.000001912242 -0.000000421396 0.000002972193 0.000025872619 0.000298637324 -0.000050387528 + 25 Si 1.097922677034 3.293768031103 7.685458739241 -0.000001881095 -0.000000388874 -0.000002976625 0.000141249645 -0.000093732207 0.000352455563 + 26 Si 1.097922677034 7.685458739241 3.293768031103 -0.000001929523 0.000000418217 0.000002988603 -0.000014113009 0.000203532178 -0.000044716871 + 27 Si 1.097922677034 7.685458739241 7.685458739241 -0.000001896186 0.000000390560 -0.000002984794 -0.000546085507 0.000611212177 -0.000299394720 + 28 Si 5.489613385188 3.293768031103 3.293768031087 0.000001912591 -0.000000430043 0.000002978352 0.000147349880 -0.000416300939 0.000288445490 + 29 Si 5.489613385172 3.293768031103 7.685458739241 0.000001878025 -0.000000392721 -0.000002970815 -0.000299483342 -0.000062120196 -0.000469594597 + 30 Si 5.489613385172 7.685458739241 3.293768031103 0.000001926448 0.000000430523 0.000002990728 -0.000345697942 -0.000154853834 0.000410983533 + 31 Si 5.489613385172 7.685458739241 7.685458739241 0.000001899104 0.000000390698 -0.000002994081 -0.000726864693 0.000016907426 0.000470482176 + 32 C 0.000000000000 0.000000000000 0.000000000016 -0.000001314476 0.000001020459 -0.000004833255 0.000615939619 -0.000424149803 0.000601059536 + 33 C 0.000000000000 0.000000000000 4.391690708122 -0.000001329119 0.000001035724 0.000004828794 -0.000418865252 -0.000327001363 -0.000475272710 + 34 C 0.000000000000 4.391690708138 0.000000000016 -0.000001321743 -0.000001022241 -0.000004837728 0.000134030627 -0.000664226072 -0.000341742540 + 35 C 0.000000000000 4.391690708122 4.391690708122 -0.000001314455 -0.000001037589 0.000004832518 0.000123024229 -0.000136375002 0.000109929783 + 36 C 4.391690708138 0.000000000000 0.000000000016 0.000001314485 0.000001052177 -0.000004858658 -0.000414174062 0.000259069389 -0.000322429034 + 37 C 4.391690708138 0.000000000000 4.391690708122 0.000001329210 0.000001050320 0.000004853447 -0.000079221522 -0.000284845598 -0.000265948466 + 38 C 4.391690708138 4.391690708122 0.000000000016 0.000001321783 -0.000001053971 -0.000004885357 0.000290940481 0.000326124214 0.000018129812 + 39 C 4.391690708138 4.391690708122 4.391690708122 0.000001314470 -0.000001051940 0.000004880841 0.000010507322 0.000342814604 0.000574253257 + 40 C 0.000000000000 2.195845354085 2.195845354085 -0.000001343006 0.000000335029 0.000000140940 -0.000075783779 -0.000353616283 -0.000090226208 + 41 C 0.000000000000 2.195845354069 6.587536062191 -0.000001333494 0.000000339239 -0.000000136425 0.000513991895 0.000227710001 0.000688262789 + 42 C 0.000000000000 6.587536062191 2.195845354085 -0.000001309324 -0.000000333114 0.000000125416 0.000071840215 -0.000538940705 -0.000533568261 + 43 C 0.000000000000 6.587536062207 6.587536062191 -0.000001294053 -0.000000337386 -0.000000120910 -0.000260079033 -0.000922768546 0.000336332844 + 44 C 4.391690708138 2.195845354069 2.195845354069 0.000001343363 0.000000372267 0.000000110673 0.000935559214 -0.000589241311 0.000120489622 + 45 C 4.391690708138 2.195845354069 6.587536062207 0.000001333173 0.000000399400 -0.000000106186 -0.000387395979 0.000114403897 0.000726197712 + 46 C 4.391690708138 6.587536062207 2.195845354069 0.000001309098 -0.000000370322 0.000000112618 0.000000130693 0.000486967692 0.000607985597 + 47 C 4.391690708138 6.587536062207 6.587536062207 0.000001294231 -0.000000397412 -0.000000108241 0.000231095926 0.000057602672 0.000011672719 + 48 C 2.195845354053 0.000000000000 2.195845354085 -0.000001891554 0.000001024505 0.000000142010 0.000872825037 0.000009549471 -0.000177890791 + 49 C 2.195845354053 0.000000000000 6.587536062191 -0.000001866474 0.000001018332 -0.000000137747 0.000064200514 0.000370053041 -0.000596854431 + 50 C 2.195845354053 4.391690708122 2.195845354069 -0.000001854566 -0.000001026207 0.000000098954 0.000190386900 -0.000569375974 0.000515671879 + 51 C 2.195845354053 4.391690708122 6.587536062207 -0.000001806433 -0.000001019864 -0.000000094424 -0.000580059013 -0.000307801019 -0.000539550807 + 52 C 6.587536062223 0.000000000000 2.195845354085 0.000001891451 0.000001058525 0.000000157125 -0.000391376095 0.000118376334 -0.000567413107 + 53 C 6.587536062223 0.000000000000 6.587536062191 0.000001866486 0.000001057329 -0.000000152449 0.000207151057 0.000030490713 0.000206357407 + 54 C 6.587536062223 4.391690708122 2.195845354069 0.000001854604 -0.000001060143 0.000000091394 -0.000901848459 0.000194781147 0.000139227901 + 55 C 6.587536062223 4.391690708122 6.587536062207 0.000001806563 -0.000001059030 -0.000000087144 -0.000369233168 -0.000322861468 0.001113396485 + 56 C 2.195845354053 2.195845354069 0.000000000016 -0.000001827680 0.000000385377 -0.000004857201 0.000213111695 -0.000008488371 -0.000218557229 + 57 C 2.195845354053 2.195845354069 4.391690708122 -0.000001858607 0.000000341406 0.000004851760 0.000334577417 -0.000754306380 0.000478375959 + 58 C 2.195845354053 6.587536062207 0.000000000016 -0.000001859961 -0.000000383101 -0.000004862670 0.000193767353 -0.000204320003 0.000921176146 + 59 C 2.195845354053 6.587536062207 4.391690708122 -0.000001872778 -0.000000339840 0.000004858586 -0.000185088786 -0.000056975950 -0.000906635613 + 60 C 6.587536062223 2.195845354069 0.000000000016 0.000001827952 0.000000392413 -0.000004846692 0.000172402199 -0.000373229717 0.000036731580 + 61 C 6.587536062223 2.195845354069 4.391690708122 0.000001858367 0.000000327064 0.000004842339 -0.000295921457 -0.000316290772 0.000761738613 + 62 C 6.587536062223 6.587536062207 0.000000000016 0.000001859650 -0.000000390850 -0.000004848435 0.000558650443 0.000541847403 -0.000256873621 + 63 C 6.587536062223 6.587536062207 4.391690708122 0.000001873135 -0.000000324768 0.000004842914 -0.000589062787 0.000653947766 0.000715648505 -MDSTEP: 5 -LATTICE_CONSTANT: 1.000000000000 +MDSTEP: 1 +LATTICE_CONSTANT: 0.999999601891 Angstrom LATTICE_VECTORS - 28.000000000000 0.000000000000 0.000000000000 - 0.000000000000 28.000000000000 0.000000000000 - 0.000000000000 0.000000000000 28.000000000000 -VIRIAL (KBAR) - 0.154743825476 -0.125714918816 0.000149755944 - -0.125714918816 0.119479071004 -0.140313773379 - 0.000149755944 -0.140313773379 0.457169606881 -INDEX LABEL POSITIONS FORCE (eV/Angstrom) - 0 H 15.972712462196 18.750422243865 8.413062924828 0.308447002711 -0.100596917061 -0.518349474860 - 1 H 13.786987486168 20.622823511243 7.605308823456 -0.219930471300 0.466062785475 -1.095536719299 - 2 O 14.510983383443 19.684685730795 8.957619837020 -0.088516531411 -0.365465868414 1.613886194160 + 8.783385481117 0.000000000000 0.000000000000 + 0.000000000000 8.783385481117 0.000000000000 + 0.000000000000 0.000000000000 8.783385481117 +VIRIAL (kbar) + 0.002490448521 0.087437217390 -0.088607004334 + 0.087437217390 0.002542393644 0.020122439375 + -0.088607004334 0.020122439375 0.002267052728 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Si 3.294017244595 1.097841453609 3.293939834061 -0.000384976126 -0.001524969998 -0.003733573501 0.000272845216 -0.000089235916 0.000187441793 + 1 Si 3.293870623402 1.097727346787 7.685801998754 -0.008643054898 0.003339028376 -0.011190411482 0.000110724579 -0.000213281117 0.000373803845 + 2 Si 3.293136389647 5.489769482259 3.293626188470 0.019030976876 -0.007593824525 0.001766878936 -0.000688140529 0.000169515887 -0.000155001711 + 3 Si 3.294380833921 5.488932816326 7.685511408932 -0.022349468467 0.015327858221 -0.004469138011 0.000666885826 -0.000742418301 0.000056838692 + 4 Si 7.685631435235 1.098380461598 3.293429396424 -0.013810137196 -0.016732034161 0.003715341362 0.000186524232 0.000498179585 -0.000370145266 + 5 Si 7.685457784236 1.097837446473 7.685534806501 0.007115465161 -0.001863519280 0.004230177222 0.000000292663 -0.000093687879 0.000084098200 + 6 Si 7.685015368562 5.489539617381 3.293765416102 0.001446658558 0.006606992898 0.000764035511 -0.000485270093 -0.000079541398 -0.000002720005 + 7 Si 7.685748988295 5.489902450325 7.684965390335 -0.008039237829 -0.017077274195 0.018592389308 0.000316344013 0.000313347359 -0.000536776701 + 8 Si 3.294363171565 3.293916426144 1.097903302446 -0.002586040792 -0.009494221587 0.007340488607 0.000651261239 0.000160723769 -0.000019836600 + 9 Si 3.293818292109 3.293560954683 5.489901118244 -0.003921640429 0.002496485040 -0.003913546375 0.000054303929 -0.000226303011 0.000314364848 + 10 Si 3.293719176139 7.685969215833 1.097834370216 0.003513057606 -0.011483783444 0.005842320456 -0.000052840992 0.000556870713 -0.000095607194 + 11 Si 3.293949535630 7.685071656842 5.489314593050 -0.004927100209 0.006372868476 0.002048194310 0.000197841635 -0.000422701232 -0.000326826648 + 12 Si 7.685378760973 3.293525759337 1.097574875491 -0.005928171135 0.007110934473 0.007590494344 -0.000088700638 -0.000263977973 -0.000379455099 + 13 Si 7.685537132398 3.294039064283 5.489501208609 0.000392687112 -0.006931542588 0.018259224951 0.000085923431 0.000295508795 -0.000119411524 + 14 Si 7.685340261785 7.685261447071 1.097374847428 0.005739369753 0.004793690432 0.016699737925 -0.000128666883 -0.000215156011 -0.000596795422 + 15 Si 7.685452289655 7.685285518434 5.490011918954 -0.002946871974 0.004059201670 -0.003538429143 -0.000007617403 -0.000188933249 0.000435775013 + 16 Si 1.097874244715 1.098596580129 1.097917304663 0.012932362334 -0.018605768194 0.003665601438 -0.000050606263 0.000734501900 -0.000005193842 + 17 Si 1.097650834729 1.097916063630 5.489823328401 0.000586955973 -0.000347439611 -0.006776845615 -0.000297588374 -0.000007307800 0.000228637346 + 18 Si 1.097925159060 5.489690539009 1.097628050588 0.002224119505 -0.013580201713 0.006345760249 0.000003136489 0.000081937800 -0.000321456363 + 19 Si 1.098132426670 5.490049388161 5.489168734826 -0.002366669438 -0.010964168256 0.005623754888 0.000229254946 0.000475411244 -0.000485885679 + 20 Si 5.489673857139 1.097669186227 1.097855721219 0.001693671106 0.001716961886 -0.004326968630 0.000066542402 -0.000277278792 -0.000074138339 + 21 Si 5.489831149672 1.098251922812 5.489439832601 -0.011947793322 -0.015102610775 0.014406776110 0.000236229809 0.000357721252 -0.000187350048 + 22 Si 5.489441142089 5.489749040399 1.097571152131 0.004200839704 0.011215335637 0.011216350806 -0.000187835883 0.000150667912 -0.000382850542 + 23 Si 5.489933381870 5.489804163996 5.489627964423 -0.005815521620 -0.006193782902 0.009446886452 0.000349339433 0.000207759768 0.000017743056 + 24 Si 1.097949345836 3.294075862161 3.293716092862 0.005583744260 -0.018856085749 0.008443893322 0.000030255793 0.000333563581 -0.000055289988 + 25 Si 1.098068274847 3.293671413204 7.685822044939 0.002584910438 0.002016821064 -0.010087135524 0.000159932709 -0.000105428394 0.000395964277 + 26 Si 1.097908129213 7.685668537403 3.293721938099 -0.001671697886 -0.001916793774 -0.016157900478 -0.000016246015 0.000229392697 -0.000053516668 + 27 Si 1.097359779492 7.686088768175 7.685150126886 0.023365494047 -0.019927374020 0.010305371592 -0.000612042629 0.000686206024 -0.000336027684 + 28 Si 5.489765271689 3.293338913910 3.294065357130 -0.008101632520 0.011054873587 0.002143268038 0.000164809284 -0.000467853438 0.000326009603 + 29 Si 5.489304682302 3.293703998416 7.684974687263 0.008131902885 -0.006505541881 0.021167143091 -0.000336535663 -0.000071346974 -0.000526111148 + 30 Si 5.489257044954 7.685299118173 3.294191667629 0.009239351547 0.010014670940 -0.010019663063 -0.000388495749 -0.000172919665 0.000462046209 + 31 Si 5.488864143654 7.685476167244 7.685943705099 0.017024241985 0.005084145621 -0.012978221864 -0.000817303715 0.000020042069 0.000528652385 + 32 C 0.000634901319 8.782944209069 0.000619561743 -0.013220850970 0.015811098487 -0.013245086780 0.000689475142 -0.000471837870 0.000672665852 + 33 C 8.782949655364 8.783044348312 4.391200805675 0.005603330367 0.007188998273 0.011837668426 -0.000470363505 -0.000365966300 -0.000531292997 + 34 C 0.000138156344 4.391006032887 8.783029150972 -0.003328731443 0.016025824093 0.007965638867 0.000149833020 -0.000742749570 -0.000382267553 + 35 C 0.000126811107 4.391550134283 4.391804024128 -0.008040659619 0.007063816353 -0.005798035867 0.000135336098 -0.000150837554 0.000121543835 + 36 C 4.391263783901 0.000267045484 8.783049059053 0.005787116527 -0.004939503562 0.008503469366 -0.000464985947 0.000290273037 -0.000360229332 + 37 C 4.391609048247 8.783087801884 4.391416574155 0.005066421704 0.008310102250 0.012680041837 -0.000087198530 -0.000317886484 -0.000294631016 + 38 C 4.391990606002 4.392026871925 0.000018686007 -0.000795195566 -0.010869177589 -0.001358114678 0.000328073098 0.000363357387 0.000019865947 + 39 C 4.391701539465 4.392044076144 4.392282642217 -0.002064280432 -0.007905283014 -0.011083794430 0.000010953568 0.000383501687 0.000643361058 + 40 C 8.783303298889 2.195480851556 2.195752350243 0.001525394707 0.017396086318 0.003438548705 -0.000084876624 -0.000391520664 -0.000100337501 + 41 C 0.000529815039 2.196080074453 6.588245513683 -0.012957858867 -0.006067023520 -0.014239506529 0.000574509182 0.000254377363 0.000770668147 + 42 C 0.000074051351 6.586980529601 2.195295359519 -0.006846814719 0.009581633850 0.012142784654 0.000078083180 -0.000604157932 -0.000596966616 + 43 C 8.783113329968 6.586584885307 6.587882749281 0.010664397030 0.023823009291 -0.014571058193 -0.000288894725 -0.001031170074 0.000373253305 + 44 C 4.392655069882 2.195237972610 2.195969553111 -0.016467227525 0.011973208624 -0.001716414664 0.001048844497 -0.000659886494 0.000135257349 + 45 C 4.391291386377 2.195963280148 6.588284616494 0.008051452956 -0.006663853202 -0.014452149829 -0.000433762056 0.000126211562 0.000813396700 + 46 C 4.391690843380 6.588038021467 2.196472057067 -0.003177457869 -0.010629531498 -0.017454766450 -0.000001249521 0.000545028011 0.000678634714 + 47 C 4.391928919069 6.587595438067 6.587548094237 -0.007170836391 -0.004434779066 0.002216340456 0.000257714396 0.000063072769 0.000014151339 + 48 C 2.196745048996 0.000009843871 2.195661986831 -0.022301808664 0.010381890302 0.003864238292 0.000975460483 0.000015346726 -0.000199108653 + 49 C 2.195911530285 0.000381445849 6.586920833030 -0.001885014302 -0.014550126963 0.010512149948 0.000071641496 0.000411327376 -0.000669123293 + 50 C 2.196041601431 4.391103803010 2.196376901388 -0.003131420708 0.009769618736 -0.016230403519 0.000213536215 -0.000638431789 0.000574966777 + 51 C 2.195247436702 4.391373430776 6.586979900829 0.013762630050 0.009236922329 0.012163472630 -0.000648735111 -0.000343392490 -0.000603710888 + 52 C 6.587132638040 0.000122021076 2.195260472744 0.009997800268 -0.008271853817 0.013384151817 -0.000437398568 0.000129988767 -0.000634625648 + 53 C 6.587749591352 0.000031429821 6.587748772425 -0.007898698722 -0.001036282531 0.000568504963 0.000230364811 0.000033963475 0.000233192386 + 54 C 6.586606450333 4.391891485348 2.195988868256 0.017884387630 -0.009602846478 -0.005251816709 -0.001010166036 0.000215650420 0.000154854596 + 55 C 6.587155462622 4.391357906662 6.588683735520 0.009638309613 0.010440114679 -0.028539598927 -0.000412561134 -0.000359863958 0.001244281762 + 56 C 2.196065025840 2.195836604531 8.783156128641 0.002751646134 0.004865032262 0.009504244461 0.000241776362 -0.000007441838 -0.000242535543 + 57 C 2.196190230975 2.195067825859 4.392183813243 -0.008940651618 0.016426319531 -0.012337044341 0.000373747536 -0.000844258147 0.000534580642 + 58 C 2.196045085953 6.587325451884 0.000949533404 -0.000697850229 0.005752199844 -0.030144971512 0.000218422593 -0.000228112534 0.001026589478 + 59 C 2.195654566398 6.587477332067 4.390756162908 -0.000615920062 0.005404133198 0.018746915218 -0.000209205480 -0.000061939254 -0.001015189209 + 60 C 6.587713772706 2.195460634314 0.000037860463 -0.009641505330 0.006461629691 -0.004306343606 0.000190372662 -0.000418470465 0.000039567395 + 61 C 6.587231031317 2.195519326146 4.392475899455 0.015095067976 0.011008838840 -0.016567886755 -0.000327404473 -0.000352195993 0.000852587883 + 62 C 6.588111911944 6.588094590688 8.783116632649 -0.015318904290 -0.013532056308 -0.000781167434 0.000623883964 0.000605701159 -0.000290312336 + 63 C 6.586928865387 6.588210142184 4.392428390423 0.017307937352 -0.014927091069 -0.011872264648 -0.000657337793 0.000731629805 0.000802625398 -MDSTEP: 10 -LATTICE_CONSTANT: 1.000000000000 +MDSTEP: 2 +LATTICE_CONSTANT: 0.999999601891 Angstrom LATTICE_VECTORS - 28.000000000000 0.000000000000 0.000000000000 - 0.000000000000 28.000000000000 0.000000000000 - 0.000000000000 0.000000000000 28.000000000000 -VIRIAL (KBAR) - -0.091192063445 0.052076615726 0.020742614517 - 0.052076615726 -0.012621430602 -0.137196630015 - 0.020742614517 -0.137196630015 0.376312058179 -INDEX LABEL POSITIONS FORCE (eV/Angstrom) - 0 H 15.993574661987 18.734845521277 8.428473898762 -0.421531963990 0.478003484039 -0.602669270783 - 1 H 13.801966849306 20.632160064055 7.593719582169 0.265214977762 0.076407086378 -0.963824371968 - 2 O 14.508725280299 19.685078876234 8.957379058834 0.156316986228 -0.554410570417 1.566493642751 + 8.783385481117 0.000000000000 0.000000000000 + 0.000000000000 8.783385481117 0.000000000000 + 0.000000000000 0.000000000000 8.783385481117 +VIRIAL (kbar) + 0.007954393242 0.195968417405 -0.199595937514 + 0.195968417405 0.008227011548 0.044671501785 + -0.199595937514 0.044671501785 0.006840720314 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Si 3.294334699418 1.097737344235 3.294157326285 -0.000950482152 -0.003538310827 -0.008636192888 0.000392434569 -0.000129516950 0.000267165328 + 1 Si 3.293997993401 1.097479716529 7.686235087107 -0.019534219699 0.007805699418 -0.025322383996 0.000153384451 -0.000304617286 0.000530275261 + 2 Si 3.292338841853 5.489965450298 3.293446110247 0.043264650715 -0.016914788994 0.004171445488 -0.000977236408 0.000238784826 -0.000221839258 + 3 Si 3.295153076733 5.488071467208 7.685576786724 -0.050714804553 0.034695638432 -0.010429536125 0.000944355723 -0.001057968092 0.000078645181 + 4 Si 7.685846128770 1.098957339098 3.292999281687 -0.030974777784 -0.038401314907 0.008336480290 0.000258957912 0.000705338801 -0.000530206139 + 5 Si 7.685459347069 1.097728098016 7.685633401591 0.015534372793 -0.003491172818 0.009469894268 0.000005233293 -0.000135986771 0.000123956927 + 6 Si 7.684450888734 5.489448186763 3.293762381964 0.003253949957 0.015297797213 0.001409802477 -0.000697472233 -0.000109833722 -0.000003453184 + 7 Si 7.686115749618 5.490264171827 7.684343915379 -0.017994154768 -0.039124399463 0.042068442569 0.000449797152 0.000439074561 -0.000759719016 + 8 Si 3.295120626251 3.294101836002 1.097881478698 -0.006513767295 -0.021722144314 0.016587609852 0.000935456068 0.000224704848 -0.000023468082 + 9 Si 3.293880814141 3.293298025596 5.490266285019 -0.008625483201 0.005793098391 -0.009088675397 0.000075496380 -0.000323966866 0.000449716978 + 10 Si 3.293658286401 7.686615296070 1.097724111835 0.008206561400 -0.025751608320 0.013520131388 -0.000073566517 0.000793618054 -0.000133498068 + 11 Si 3.294178925553 7.684580837106 5.488934603559 -0.011214201481 0.014415885587 0.004300943260 0.000281333008 -0.000603996089 -0.000469067277 + 12 Si 7.685274518170 3.293219779023 1.097134592176 -0.012806470491 0.016116292806 0.016102752511 -0.000131651036 -0.000375020555 -0.000541132928 + 13 Si 7.685637192404 3.294381769098 5.489365381067 0.000720782784 -0.015403701523 0.041927069386 0.000123909989 0.000420593780 -0.000159087512 + 14 Si 7.685191512830 7.685011884796 1.096683201164 0.012465002553 0.010785289413 0.037929955846 -0.000181328393 -0.000306373828 -0.000847387979 + 15 Si 7.685442918782 7.685066346476 5.490518440057 -0.006544069739 0.009377416389 -0.008284781792 -0.000012980457 -0.000269085391 0.000624718531 + 16 Si 1.097817573609 1.099448153555 1.097911890033 0.029267326410 -0.041488271984 0.008207179296 -0.000063874357 0.001044434135 -0.000004953309 + 17 Si 1.097304619992 1.097907499568 5.490088238794 0.001576165514 -0.000793093403 -0.015463043441 -0.000427872660 -0.000010760754 0.000324362978 + 18 Si 1.097929191163 5.489783560603 1.097255048922 0.004743027418 -0.030663453875 0.013908507694 0.000005994687 0.000108536988 -0.000458383385 + 19 Si 1.098398813341 5.490600759994 5.488604256131 -0.005365759423 -0.024901794476 0.012915089680 0.000328334087 0.000676660746 -0.000695418284 + 20 Si 5.489751586136 1.097346800672 1.097768700192 0.003723228486 0.003319293183 -0.009882811422 0.000096928290 -0.000398029764 -0.000109729546 + 21 Si 5.490104007488 1.098665623192 5.489224280518 -0.026968047593 -0.033839080578 0.032744379758 0.000331748275 0.000504486298 -0.000259643829 + 22 Si 5.489223271510 5.489926305207 1.097127540228 0.009854737274 0.025869498115 0.025601422146 -0.000267374403 0.000224741873 -0.000543231783 + 23 Si 5.490338923267 5.490044878467 5.489650235455 -0.013488478404 -0.014362030933 0.021016102764 0.000498718620 0.000294670738 0.000032010358 + 24 Si 1.097985514858 3.294460804540 3.293653200117 0.012895019471 -0.042403662573 0.018786250302 0.000047474401 0.000467098063 -0.000073796192 + 25 Si 1.098254838993 3.293549068377 7.686281111792 0.005384078187 0.004800503298 -0.022609318280 0.000231891328 -0.000150299424 0.000562982557 + 26 Si 1.097888935918 7.685935161658 3.293656883100 -0.003681955844 -0.004080584272 -0.036304647016 -0.000024521020 0.000328900977 -0.000088174810 + 27 Si 1.096651534441 7.686883910731 7.684760848144 0.052655058305 -0.045150408205 0.022989490263 -0.000864789390 0.000973860910 -0.000476586010 + 28 Si 5.489955675236 3.292796352980 3.294445115775 -0.018830388463 0.025210818338 0.005157458583 0.000231495538 -0.000665697535 0.000470791237 + 29 Si 5.488914439060 3.293619851593 7.684366066514 0.018954503840 -0.014881570812 0.047105916204 -0.000478636179 -0.000107236661 -0.000742750361 + 30 Si 5.488806523901 7.685099604860 3.294727648274 0.020707526316 0.022457777044 -0.023259266913 -0.000552816930 -0.000241992085 0.000657973480 + 31 Si 5.487915938761 7.685500364327 7.686556689829 0.038630766867 0.011651561621 -0.029013675625 -0.001164557572 0.000032403013 0.000751991617 + 32 C 0.001431961074 8.782401462944 0.001397050116 -0.029799567322 0.035670117269 -0.028977212220 0.000971020839 -0.000653562684 0.000947222965 + 33 C 8.782404525032 8.782621346095 4.390587273285 0.012738080664 0.015830928559 0.026195767157 -0.000667903613 -0.000515315885 -0.000745819632 + 34 C 0.000311186059 4.390148102166 8.782587490271 -0.007275111455 0.035459743008 0.017033033041 0.000210393620 -0.001043495821 -0.000537796014 + 35 C 0.000281077608 4.391377435760 4.391943140776 -0.017568727882 0.016259495661 -0.012410470989 0.000182073164 -0.000205520768 0.000165897921 + 36 C 4.390724985467 0.000602863923 8.782633261138 0.013336470784 -0.011046718092 0.019781619026 -0.000659774888 0.000409861368 -0.000504442807 + 37 C 4.391509606757 8.782721202379 4.391078793174 0.011009555201 0.018655901662 0.027711811587 -0.000117522581 -0.000444152145 -0.000404009878 + 38 C 4.392372078469 4.392445359888 0.000041259317 -0.001676572328 -0.024409430612 -0.003481813500 0.000470982334 0.000505470945 0.000026189585 + 39 C 4.391713457448 4.392487197299 4.393026895513 -0.004731555701 -0.017566627404 -0.024560041156 0.000012389954 0.000539337265 0.000908311287 + 40 C 8.783205137228 2.195032210411 2.195636964562 0.004423654880 0.038807029409 0.006799357346 -0.000119211369 -0.000535612821 -0.000139334300 + 41 C 0.001193189914 2.196373666781 6.589136651856 -0.029287469641 -0.012902730522 -0.030799375316 0.000805930249 0.000356712977 0.001086882830 + 42 C 0.000162169842 6.586281295212 2.194605522649 -0.015882368754 0.021679117551 0.026739999362 0.000101097300 -0.000854061889 -0.000839924665 + 43 C 8.782781414949 6.585394439811 6.588311266649 0.024261135468 0.052423157322 -0.032584166319 -0.000398468913 -0.001446331858 0.000513814569 + 44 C 4.393869038291 2.194474845235 2.196126268125 -0.037062520372 0.025573663139 -0.003301337385 0.001483056407 -0.000931151703 0.000192189240 + 45 C 4.390789833920 2.196107481059 6.589225394195 0.018474715529 -0.014714167592 -0.032454281214 -0.000611155526 0.000171041852 0.001147456191 + 46 C 4.391688113025 6.588668023097 2.197254800813 -0.006643896874 -0.022890123661 -0.038659582248 -0.000006677502 0.000767831386 0.000948912982 + 47 C 4.392225951487 6.587667057141 6.587565452921 -0.016417945775 -0.010140873210 0.004534059125 0.000359221497 0.000083542622 0.000023722088 + 48 C 2.197871273996 0.000031873396 2.195431828167 -0.049102823962 0.023758989482 0.008926594623 0.001368551714 0.000039049585 -0.000280231794 + 49 C 2.195994145254 0.000854279952 6.586146369582 -0.003991988019 -0.032462785102 0.023081897885 0.000100197251 0.000568686975 -0.000946410306 + 50 C 2.196288844367 4.390364758259 2.197039494354 -0.006990089731 0.021484909103 -0.036263845172 0.000302324082 -0.000903396871 0.000801497471 + 51 C 2.194498005367 4.390977521166 6.586282223688 0.030151935329 0.020627045554 0.027067177588 -0.000911937704 -0.000479424440 -0.000849459186 + 52 C 6.586627635384 0.000269971813 2.194527309143 0.021869348354 -0.019675920594 0.029431208951 -0.000613736452 0.000173214858 -0.000892175382 + 53 C 6.588014503608 0.000070538256 6.588020376127 -0.017839482628 -0.001485161628 0.001596331550 0.000318788249 0.000047632553 0.000336719645 + 54 C 6.585438062812 4.392138589398 2.196166969368 0.039427402042 -0.020271884645 -0.011839624874 -0.001425505947 0.000295554232 0.000214398518 + 55 C 6.586679219896 4.390943311808 6.590120293225 0.021617718370 0.022397018204 -0.062912989162 -0.000578290415 -0.000501655564 0.001745518840 + 56 C 2.196347495926 2.195829898223 8.782877697687 0.005534093711 0.011065086657 0.021524230725 0.000352115660 -0.000002797674 -0.000333678038 + 57 C 2.196621584972 2.194091926384 4.392800971022 -0.019290818460 0.036231384942 -0.027788840296 0.000523926798 -0.001189019355 0.000749512208 + 58 C 2.196298992816 6.587062298544 0.002132109039 -0.001504806828 0.012564059677 -0.067047347621 0.000313291157 -0.000319233476 0.001429333264 + 59 C 2.195410858179 6.587407421454 4.389582276156 -0.001139323024 0.012246798885 0.041653542255 -0.000301990744 -0.000080383379 -0.001431201648 + 60 C 6.587931444486 2.194976238738 0.000082176974 -0.021168500790 0.014216436661 -0.010893603962 0.000258706206 -0.000592050852 0.000049400154 + 61 C 6.586856080550 2.195113883242 4.393461435718 0.033096101634 0.024618931252 -0.035966522956 -0.000447307667 -0.000489232399 0.001201069966 + 62 C 6.588831797916 6.588794034293 8.782778470748 -0.034072529161 -0.029861022598 -0.001153818855 0.000873447565 0.000850256079 -0.000418820753 + 63 C 6.586170846751 6.589055573697 4.393357669346 0.037876189338 -0.032827545306 -0.026943748107 -0.000918721484 0.001029344082 0.001135971697 -MDSTEP: 15 -LATTICE_CONSTANT: 1.000000000000 +MDSTEP: 3 +LATTICE_CONSTANT: 0.999999601891 Angstrom LATTICE_VECTORS - 28.000000000000 0.000000000000 0.000000000000 - 0.000000000000 28.000000000000 0.000000000000 - 0.000000000000 0.000000000000 28.000000000000 -VIRIAL (KBAR) - -0.247917742642 0.164910534300 0.034034337680 - 0.164910534300 -0.098300168752 -0.128317310754 - 0.034034337680 -0.128317310754 0.301502887031 -INDEX LABEL POSITIONS FORCE (eV/Angstrom) - 0 H 16.013474681966 18.720459436062 8.442030452618 -0.543198631066 0.457161183663 -0.206821526696 - 1 H 13.816825157151 20.642826422172 7.577781781099 0.022709639914 0.211549051866 -0.758980258266 - 2 O 14.506535423527 19.685313227829 8.957529083034 0.520488991152 -0.668710235529 0.965801784963 - - -MDSTEP: 20 -LATTICE_CONSTANT: 1.000000000000 -LATTICE_VECTORS - 28.000000000000 0.000000000000 0.000000000000 - 0.000000000000 28.000000000000 0.000000000000 - 0.000000000000 0.000000000000 28.000000000000 -VIRIAL (KBAR) - -0.404277528792 0.286670843238 0.018904177312 - 0.286670843238 -0.202681869786 -0.083866196906 - 0.018904177312 -0.083866196906 0.189108946079 -INDEX LABEL POSITIONS FORCE (eV/Angstrom) - 0 H 16.030788395118 18.708219053395 8.454627488439 -0.812329959008 0.587918500063 0.000941318509 - 1 H 13.831803451625 20.654370023278 7.558509583331 0.039826431878 0.100785737160 -0.450166047811 - 2 O 14.504500950754 19.685357126714 8.957949634007 0.772503527130 -0.688704237222 0.449224729302 + 8.783385481117 0.000000000000 0.000000000000 + 0.000000000000 8.783385481117 0.000000000000 + 0.000000000000 0.000000000000 8.783385481117 +VIRIAL (kbar) + 0.025289496702 0.365191114081 -0.374927324624 + 0.365191114081 0.026275263036 0.081979394917 + -0.374927324624 0.081979394917 0.021407465814 +INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) + 0 Si 3.294850205578 1.097566547740 3.294506905139 -0.001897954425 -0.006191127425 -0.016497162292 0.000718639106 -0.000239732247 0.000483684352 + 1 Si 3.294196189173 1.097080782153 7.686927533140 -0.037019016982 0.014800347659 -0.048161981127 0.000267598605 -0.000552938319 0.000954372055 + 2 Si 3.291062159031 5.490276314375 3.293155324126 0.081574044995 -0.031756175081 0.007349685860 -0.001761334278 0.000426023796 -0.000403864577 + 3 Si 3.296385273725 5.486687228883 7.685678337059 -0.095227064962 0.065944042482 -0.019662278683 0.001696008332 -0.001915111571 0.000136944073 + 4 Si 7.686181085683 1.099877576650 3.292304008752 -0.058118618641 -0.072100340728 0.015958621647 0.000453314813 0.001266388867 -0.000966031680 + 5 Si 7.685468892148 1.097548808103 7.685797910957 0.028873561002 -0.006478226444 0.017401552498 0.000020233141 -0.000251648745 0.000233648305 + 6 Si 7.683534950673 5.489306490098 3.293758086556 0.006490736175 0.028464563905 0.002093359649 -0.001276112217 -0.000190836176 -0.000005490191 + 7 Si 7.686703704080 5.490834406902 7.683352850698 -0.034502950390 -0.073269968011 0.079208919720 0.000811886719 0.000777880424 -0.001363484300 + 8 Si 3.296348721430 3.294393372839 1.097853490329 -0.012263813857 -0.040495541019 0.030667925131 0.001710165565 0.000396969635 -0.000031693361 + 9 Si 3.293978536756 3.292873319647 5.490855663856 -0.016373134142 0.010966960344 -0.017255236288 0.000132392799 -0.000589806327 0.000818006373 + 10 Si 3.293563027717 7.687653707785 1.097551014236 0.015013581640 -0.048686977940 0.024568207716 -0.000129281557 0.001436843410 -0.000235571825 + 11 Si 3.294546678280 7.683789646501 5.488318975511 -0.021102394267 0.027611630353 0.008823777695 0.000507932125 -0.001097037707 -0.000856642405 + 12 Si 7.685099325406 3.292729760425 1.096426295190 -0.024213620666 0.030360435548 0.030358391791 -0.000250183126 -0.000676265855 -0.000980748937 + 13 Si 7.685800137226 3.294931794526 5.489163537821 0.001381218683 -0.029073596457 0.078050481478 0.000227627220 0.000760279392 -0.000262854949 + 14 Si 7.684955383672 7.684611154092 1.095576226260 0.023756440952 0.020779859914 0.071117018251 -0.000323690807 -0.000554011307 -0.001527109609 + 15 Si 7.685424738020 7.684714371932 5.491337913661 -0.012394502020 0.018171603904 -0.015850738209 -0.000028330719 -0.000486624951 0.001139308498 + 16 Si 1.097738668363 1.100813441107 1.097906791031 0.054776132792 -0.077995823262 0.014770595946 -0.000096942119 0.001885788863 -0.000003573533 + 17 Si 1.096742654717 1.097893223419 5.490511804204 0.003458900574 -0.001452396560 -0.029135114768 -0.000783072197 -0.000020262208 0.000583862056 + 18 Si 1.097937883067 5.489920913912 1.096655110117 0.009179764284 -0.056908779481 0.025875936307 0.000014324158 0.000177961940 -0.000830671146 + 19 Si 1.098829331339 5.491485632682 5.487692676541 -0.010286339575 -0.046877922210 0.024550032876 0.000598076801 0.001223101023 -0.001265705246 + 20 Si 5.489879592032 1.096824349177 1.097622815055 0.006625740075 0.006758016581 -0.018802898823 0.000180146588 -0.000727162820 -0.000208004630 + 21 Si 5.490535301118 1.099322718902 5.488888726262 -0.050661440407 -0.063921046944 0.061714740898 0.000589484406 0.000901284848 -0.000453286388 + 22 Si 5.488873627239 5.490226065681 1.096418116912 0.018535408536 0.047854142710 0.047798614627 -0.000483287216 0.000429610634 -0.000978141205 + 23 Si 5.490991935790 5.490429616611 5.489695907924 -0.026007388140 -0.026651992255 0.039476617858 0.000904673654 0.000530295808 0.000073168857 + 24 Si 1.098050112502 3.295067299948 3.293559456945 0.023761166968 -0.079334250151 0.034927337934 0.000095802504 0.000827007897 -0.000122395959 + 25 Si 1.098560475187 3.293352395549 7.687017002112 0.010584794536 0.009075035230 -0.042982969688 0.000428876667 -0.000272169913 0.001016214651 + 26 Si 1.097856082185 7.686366645324 3.293534782884 -0.007031922341 -0.007427276705 -0.068222913642 -0.000047513516 0.000600108904 -0.000186667995 + 27 Si 1.095524223004 7.688155834137 7.684138550479 0.099099358769 -0.084531645433 0.042760183994 -0.001548772707 0.001753986559 -0.000857814479 + 28 Si 5.490256631947 3.291925939323 3.295064633856 -0.035205875887 0.047557484983 0.008783637388 0.000411377147 -0.001202768886 0.000866287662 + 29 Si 5.488288754315 3.293476383517 7.683398164400 0.035206817886 -0.027629224652 0.088911698181 -0.000864349086 -0.000206747895 -0.001328849291 + 30 Si 5.488083664806 7.684785478497 3.295588247543 0.039160707461 0.042332102281 -0.043923688380 -0.000998952891 -0.000428040332 0.001189949223 + 31 Si 5.486392314985 7.685544944175 7.687539842966 0.072674021493 0.021746479708 -0.055151655590 -0.002107931631 0.000067396381 0.001358212670 + 32 C 0.002695939096 8.781556991280 0.002630087403 -0.053689427963 0.065704331668 -0.052876212534 0.001733077109 -0.001141164342 0.001690372643 + 33 C 8.781531998274 8.781950565909 4.389617768139 0.023040640382 0.029456394011 0.048070793321 -0.001204202684 -0.000919186177 -0.001325456699 + 34 C 0.000584726779 4.388791163526 8.781887653430 -0.013417106572 0.065437176966 0.031277378038 0.000374052253 -0.001856168459 -0.000958697857 + 35 C 0.000513270031 4.391113906706 4.392156150333 -0.032548549529 0.030290080147 -0.023352493264 0.000305655443 -0.000350633152 0.000284049076 + 36 C 4.389863380414 0.001136995672 8.781978355274 0.024393320828 -0.020286784497 0.036468522521 -0.001188209817 0.000733708999 -0.000893113905 + 37 C 4.391359600996 8.782145067894 4.390559044031 0.020430220938 0.034955852361 0.051853167740 -0.000197800611 -0.000784081033 -0.000695960363 + 38 C 4.392990288341 4.393099757976 0.000074274644 -0.003145060501 -0.045590347727 -0.006569008827 0.000860596035 0.000887294840 0.000042373529 + 39 C 4.391727837729 4.393188845065 4.394210575997 -0.009043785666 -0.032310219052 -0.045126652842 0.000014992424 0.000960645289 0.001625865370 + 40 C 8.783050267105 2.194343987945 2.195456606583 0.007960381923 0.072323525715 0.012305045280 -0.000211572617 -0.000919499403 -0.000244692118 + 41 C 0.002240440210 2.196837214662 6.590552474030 -0.053093699272 -0.024223460837 -0.056230707424 0.001431091350 0.000633043967 0.001943464916 + 42 C 0.000288635166 6.585167742743 2.193512579587 -0.029067029997 0.039985760482 0.048459864634 0.000160124390 -0.001530922178 -0.001497425692 + 43 C 8.782267560804 6.583514977354 6.588973345068 0.045055501003 0.096800032378 -0.060155603331 -0.000691545847 -0.002567479555 0.000889847760 + 44 C 4.395802927433 2.193261558965 2.196377483887 -0.066486373755 0.046183938160 -0.006157583093 0.002660384917 -0.001666570932 0.000346977897 + 45 C 4.389994179792 2.196326324591 6.590720146672 0.033068170727 -0.027487538086 -0.059149288660 -0.001091352714 0.000289870275 0.002051931775 + 46 C 4.391676670066 6.589667779995 2.198486169869 -0.013101248778 -0.041736479048 -0.071703824582 -0.000023302438 0.001371204684 0.001677496891 + 47 C 4.392691383731 6.587772761243 6.587598445493 -0.030639551615 -0.018508294527 0.008558014661 0.000632077725 0.000137079809 0.000050817122 + 48 C 2.199649864906 0.000092728467 2.195067181559 -0.089883802878 0.044237861322 0.015917239097 0.002430646038 0.000109673916 -0.000499737621 + 49 C 2.196124203701 0.001588510922 6.584912032276 -0.007098576940 -0.059699759841 0.042688551481 0.000177444972 0.000990750758 -0.001697893993 + 50 C 2.196683298631 4.389186300311 2.198078117778 -0.012009911755 0.039429294036 -0.067289563167 0.000543506337 -0.001621772413 0.001411103860 + 51 C 2.193311805680 4.390355829668 6.585176883426 0.055595775781 0.037627865446 0.049511815225 -0.001623513863 -0.000846132708 -0.001514129508 + 52 C 6.585829953317 0.000489677826 2.193366788188 0.040216331038 -0.036093087634 0.053842545765 -0.001090176588 0.000286251878 -0.001588676179 + 53 C 6.588426234528 0.000132532173 6.588463475839 -0.033601086947 -0.003000027812 0.003018371344 0.000555508972 0.000084796190 0.000619783236 + 54 C 6.583580746363 4.392518813220 2.196443939277 0.071098559306 -0.037488783001 -0.022148018298 -0.002550987433 0.000509380656 0.000373943989 + 55 C 6.585928013794 4.390293118940 6.592388682030 0.039314700791 0.041652898769 -0.114500420932 -0.001025851136 -0.000883634926 0.003100086602 + 56 C 2.196812408026 2.195830666336 8.782447881182 0.010885038569 0.020375871574 0.039628978724 0.000654617461 0.000012487608 -0.000577359765 + 57 C 2.197302290449 2.192544075895 4.393774688448 -0.034974041352 0.065872167368 -0.050356220010 0.000929939827 -0.002122232990 0.001330052052 + 58 C 2.196710061290 6.586647863692 0.003983361036 -0.001846717202 0.023286930555 -0.122764130731 0.000572376172 -0.000565059554 0.002513580895 + 59 C 2.195013576722 6.587306714533 4.387718369543 -0.002199498333 0.023174228451 0.075358093887 -0.000555411282 -0.000127494883 -0.002557793716 + 60 C 6.588262888896 2.194203978305 0.000142714632 -0.039811789410 0.026257254997 -0.020022560378 0.000440035370 -0.001062536201 0.000073227469 + 61 C 6.586281599583 2.194480907180 4.395025227413 0.061270930249 0.045423005624 -0.066369597169 -0.000767030744 -0.000857506416 0.002144191123 + 62 C 6.589965845821 6.589899299536 8.782227665741 -0.063191099193 -0.054579085898 -0.003574393347 0.001546510400 0.001511185784 -0.000770335875 + 63 C 6.584978835471 6.590394973809 4.394839544219 0.068672426001 -0.059110996918 -0.048132803085 -0.001624294060 0.001835247894 0.002040140738 diff --git a/tests/abacus.md/OUT.abacus/running_md.log b/tests/abacus.md/OUT.abacus/running_md.log index c099ca4da..52c44ad1e 100644 --- a/tests/abacus.md/OUT.abacus/running_md.log +++ b/tests/abacus.md/OUT.abacus/running_md.log @@ -1,27 +1,28 @@ - WELCOME TO ABACUS - - 'Atomic-orbital Based Ab-initio Computation at UStc' - + ABACUS v3.2 + + Atomic-orbital Based Ab-initio Computation at UStc + Website: http://abacus.ustc.edu.cn/ - - Version: Parallel, in development - Processor Number is 4 - Start Time is Wed Apr 13 14:58:14 2022 + Documentation: https://abacus.deepmodeling.com/ + Repository: https://github.com/abacusmodeling/abacus-develop + https://github.com/deepmodeling/abacus-develop + + Start Time is Thu Apr 27 10:51:21 2023 ------------------------------------------------------------------------------------ READING GENERAL INFORMATION - global_out_dir = OUT.abacus/ + global_out_dir = OUT.ABACUS/ global_in_card = INPUT pseudo_dir = orbital_dir = - pseudo_type = auto DRANK = 1 - DSIZE = 4 + DSIZE = 16 DCOLOR = 1 GRANK = 1 GSIZE = 1 + The esolver type has been set to : ksdft_lcao @@ -45,51 +46,168 @@ READING UNITCELL INFORMATION ntype = 2 - atom label for species 1 = H - atom label for species 2 = O - lattice constant (Bohr) = 1 - lattice constant (Angstrom) = 0.529177 + lattice constant (Bohr) = 1.88973 + lattice constant (Angstrom) = 1 READING ATOM TYPE 1 - atom label = H - L=0, number of zeta = 2 - L=1, number of zeta = 1 - number of atom for this type = 2 + atom label = Si + L=0, number of zeta = 3 + L=1, number of zeta = 3 + L=2, number of zeta = 2 + number of atom for this type = 32 + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE start magnetization = FALSE start magnetization = FALSE READING ATOM TYPE 2 - atom label = O - L=0, number of zeta = 2 - L=1, number of zeta = 2 - L=2, number of zeta = 1 - number of atom for this type = 1 + atom label = C + L=0, number of zeta = 3 + L=1, number of zeta = 3 + L=2, number of zeta = 2 + number of atom for this type = 32 + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE start magnetization = FALSE - TOTAL ATOM NUMBER = 3 + TOTAL ATOM NUMBER = 64 - CARTESIAN COORDINATES ( UNIT = 1 Bohr ). + CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ). atom x y z mag vx vy vz - tauc_H1 15.9532129411 18.7655861467 8.39524747132 0 0 0 0 - tauc_H2 13.7711312041 20.6154930027 7.61198952454 0 0 0 0 - tauc_O1 14.5132108826 19.6841922084 8.95832135273 0 0 0 0 - - - READING ORBITAL FILE NAMES FOR LCAO - orbital file: H_gga_8au_60Ry_2s1p.orb - orbital file: O_gga_7au_60Ry_2s2p1d.orb - - Volume (Bohr^3) = 21952 - Volume (A^3) = 3252.94689686 + tauc_Si1 3.2937695554 1.09792318514 3.29376955542 0 0 0 0 + tauc_Si2 3.29376955542 1.09792318514 7.68546229598 0 0 0 0 + tauc_Si3 3.2937695554 5.4896159257 3.2937695554 0 0 0 0 + tauc_Si4 3.2937695554 5.4896159257 7.68546229599 0 0 0 0 + tauc_Si5 7.68546229599 1.09792318514 3.29376955542 0 0 0 0 + tauc_Si6 7.68546229598 1.09792318514 7.68546229598 0 0 0 0 + tauc_Si7 7.68546229599 5.48961592568 3.29376955542 0 0 0 0 + tauc_Si8 7.68546229599 5.4896159257 7.68546229598 0 0 0 0 + tauc_Si9 3.2937695554 3.29376955542 1.09792318516 0 0 0 0 + tauc_Si10 3.2937695554 3.2937695554 5.48961592568 0 0 0 0 + tauc_Si11 3.29376955542 7.68546229598 1.09792318516 0 0 0 0 + tauc_Si12 3.2937695554 7.68546229599 5.48961592568 0 0 0 0 + tauc_Si13 7.68546229599 3.29376955542 1.09792318516 0 0 0 0 + tauc_Si14 7.68546229599 3.29376955542 5.48961592568 0 0 0 0 + tauc_Si15 7.68546229598 7.68546229598 1.09792318516 0 0 0 0 + tauc_Si16 7.68546229599 7.68546229598 5.48961592568 0 0 0 0 + tauc_Si17 1.09792318514 1.09792318516 1.09792318516 0 0 0 0 + tauc_Si18 1.09792318514 1.09792318514 5.48961592568 0 0 0 0 + tauc_Si19 1.09792318514 5.48961592568 1.09792318516 0 0 0 0 + tauc_Si20 1.09792318512 5.4896159257 5.48961592568 0 0 0 0 + tauc_Si21 5.4896159257 1.09792318514 1.09792318516 0 0 0 0 + tauc_Si22 5.4896159257 1.09792318514 5.48961592568 0 0 0 0 + tauc_Si23 5.4896159257 5.4896159257 1.09792318516 0 0 0 0 + tauc_Si24 5.48961592571 5.4896159257 5.48961592568 0 0 0 0 + tauc_Si25 1.09792318514 3.29376955542 3.29376955542 0 0 0 0 + tauc_Si26 1.09792318514 3.29376955542 7.68546229598 0 0 0 0 + tauc_Si27 1.09792318514 7.68546229598 3.29376955542 0 0 0 0 + tauc_Si28 1.09792318514 7.68546229598 7.68546229598 0 0 0 0 + tauc_Si29 5.48961592571 3.29376955542 3.2937695554 0 0 0 0 + tauc_Si30 5.4896159257 3.29376955542 7.68546229598 0 0 0 0 + tauc_Si31 5.4896159257 7.68546229598 3.29376955542 0 0 0 0 + tauc_Si32 5.4896159257 7.68546229598 7.68546229598 0 0 0 0 + tauc_C1 4.47161680412e-27 1.35112387452e-27 1.59768851174e-11 0 0 0 0 + tauc_C2 1.22914866777e-15 3.71394102648e-16 4.39169274054 0 0 0 0 + tauc_C3 2.68589019106e-15 4.39169274056 1.59772565115e-11 0 0 0 0 + tauc_C4 3.91503885881e-15 4.39169274054 4.39169274054 0 0 0 0 + tauc_C5 4.39169274056 2.68589019105e-15 1.59781142661e-11 0 0 0 0 + tauc_C6 4.39169274056 3.0572842937e-15 4.39169274054 0 0 0 0 + tauc_C7 4.39169274056 4.39169274054 1.59784856602e-11 0 0 0 0 + tauc_C8 4.39169274056 4.39169274054 4.39169274054 0 0 0 0 + tauc_C9 1.95751942943e-15 2.1958463703 2.1958463703 0 0 0 0 + tauc_C10 3.18666809718e-15 2.19584637028 6.58753911082 0 0 0 0 + tauc_C11 4.64340962046e-15 6.58753911082 2.1958463703 0 0 0 0 + tauc_C12 5.87255828823e-15 6.58753911084 6.58753911082 0 0 0 0 + tauc_C13 4.39169274056 2.19584637028 2.19584637028 0 0 0 0 + tauc_C14 4.39169274056 2.19584637028 6.58753911084 0 0 0 0 + tauc_C15 4.39169274056 6.58753911084 2.19584637028 0 0 0 0 + tauc_C16 4.39169274056 6.58753911084 6.58753911084 0 0 0 0 + tauc_C17 2.19584637026 1.52864214684e-15 2.1958463703 0 0 0 0 + tauc_C18 2.19584637026 1.90003624949e-15 6.58753911082 0 0 0 0 + tauc_C19 2.19584637026 4.39169274054 2.19584637028 0 0 0 0 + tauc_C20 2.19584637026 4.39169274054 6.58753911084 0 0 0 0 + tauc_C21 6.58753911085 4.21453233791e-15 2.1958463703 0 0 0 0 + tauc_C22 6.58753911085 4.58592644056e-15 6.58753911082 0 0 0 0 + tauc_C23 6.58753911085 4.39169274054 2.19584637028 0 0 0 0 + tauc_C24 6.58753911085 4.39169274054 6.58753911084 0 0 0 0 + tauc_C25 2.19584637026 2.19584637028 1.59776853888e-11 0 0 0 0 + tauc_C26 2.19584637026 2.19584637028 4.39169274054 0 0 0 0 + tauc_C27 2.19584637026 6.58753911084 1.59780567829e-11 0 0 0 0 + tauc_C28 2.19584637026 6.58753911084 4.39169274054 0 0 0 0 + tauc_C29 6.58753911085 2.19584637028 1.59789145375e-11 0 0 0 0 + tauc_C30 6.58753911085 2.19584637028 4.39169274054 0 0 0 0 + tauc_C31 6.58753911085 6.58753911084 1.59792859316e-11 0 0 0 0 + tauc_C32 6.58753911085 6.58753911084 4.39169274054 0 0 0 0 + + + Volume (Bohr^3) = 4572.80236311 + Volume (A^3) = 677.618588604 Lattice vectors: (Cartesian coordinate: in unit of a_0) - +28 +0 +0 - +0 +28 +0 - +0 +0 +28 + +8.78338548112 +5.3717803821e-15 +2.45829733555e-15 + +5.3717803821e-15 +8.78338548112 +7.42788205298e-16 + +2.45829733555e-15 +7.42788205298e-16 +8.78338548112 Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) - +0.0357142857143 +0 +0 - +0 +0.0357142857143 +0 - +0 -0 +0.0357142857143 + +0.11385131646 -6.96296740648e-17 -3.18647506139e-17 + -6.96296740648e-17 +0.11385131646 -9.6281115301e-18 + -3.18647506139e-17 -9.6281115301e-18 +0.11385131646 @@ -114,23 +232,25 @@ PAO radial cut off (Bohr) = 15 - Read in pseudopotential file is H_ONCV_PBE-1.0.upf + Read in pseudopotential file is Si_ONCV_PBE-1.0.upf pseudopotential type = NC exchange-correlation functional = PBE nonlocal core correction = 0 - valence electrons = 1 - lmax = 0 + valence electrons = 4 + lmax = 1 number of zeta = 0 - number of projectors = 2 + number of projectors = 4 L of projector = 0 L of projector = 0 + L of projector = 1 + L of projector = 1 PAO radial cut off (Bohr) = 15 - Read in pseudopotential file is O_ONCV_PBE-1.0.upf + Read in pseudopotential file is C_ONCV_PBE-1.0.upf pseudopotential type = NC exchange-correlation functional = PBE nonlocal core correction = 0 - valence electrons = 6 + valence electrons = 4 lmax = 1 number of zeta = 0 number of projectors = 4 @@ -139,53 +259,69 @@ L of projector = 1 L of projector = 1 initial pseudo atomic orbital number = 0 - NLOCAL = 23 - - SETUP THE ELECTRONS NUMBER - electron number of element H = 1 - total electron number of element H = 2 - electron number of element O = 6 - total electron number of element O = 6 - occupied bands = 4 - NLOCAL = 23 - NBANDS = 6 - NBANDS = 6 - DONE : SETUP UNITCELL Time : 0.0345590766519 (SEC) - + NLOCAL = 1408 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | | - | Setup K-points | - | We setup the k-points according to input parameters. | - | The reduced k-points are set according to symmetry operations. | - | We treat the spin as another set of k-points. | - | | + | Setup plane waves of charge/potential: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. The number of plane waves | + | is 'npw' in each processor. | <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - SETUP K-POINTS - nspin = 1 - Input type of k points = Monkhorst-Pack(Gamma) - nkstot = 1 - - KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT - 1 0 0 0 1 + SETUP THE PLANE WAVE BASIS + energy cutoff for charge/potential (unit:Ry) = 400 + [fft grid for charge/potential] = 108, 108, 108 + [fft grid division] = 4, 4, 4 + [big fft grid for charge/potential] = 27, 27, 27 + nbxx = 1458 + nrxx = 93312 - k-point number in this process = 1 - minimum distributed K point number = 1 + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 617989 + number of sticks = 8765 - KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT - 1 0 0 0 2 + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 548 38626 + 2 548 38626 + 3 548 38626 + 4 548 38626 + 5 547 38623 + 6 547 38623 + 7 548 38624 + 8 548 38624 + 9 548 38624 + 10 548 38624 + 11 548 38624 + 12 548 38624 + 13 547 38623 + 14 548 38624 + 15 548 38624 + 16 548 38624 + --------------- sum ------------------- + 16 8765 617989 + number of |g| = 2269 + max |g| = 36.1643211044 + min |g| = 0.0259242445193 - KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT - 1 0 0 0 2 - DONE : INIT K-POINTS Time : 0.0349359968677 (SEC) + SETUP THE ELECTRONS NUMBER + electron number of element Si = 4 + total electron number of element Si = 128 + electron number of element C = 4 + total electron number of element C = 128 + AUTOSET number of electrons: = 256 + DONE : SETUP UNITCELL Time : 0.115999643847 (SEC) @@ -193,12 +329,10 @@ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | | - | Setup plane waves: | - | Use the energy cutoff and the lattice vectors to generate the | - | dimensions of FFT grid. The number of FFT grid on each processor | - | is 'nrxx'. The number of plane wave basis in reciprocal space is | - | different for charege/potential and wave functions. We also set | - | the 'sticks' for the parallel of FFT. | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | | | <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @@ -206,54 +340,176 @@ - SETUP THE PLANE WAVE BASIS - energy cutoff for wavefunc (unit:Ry) = 50 - [fft grid for wave functions] = 128, 128, 128 - [fft grid for charge/potential] = 128, 128, 128 - [fft grid division] = 2, 2, 2 - [big fft grid for charge/potential] = 64, 64, 64 - nbxx = 65536 - nrxx = 524288 - - SETUP PLANE WAVES FOR CHARGE/POTENTIAL - number of plane waves = 1048171 - number of sticks = 12469 - - SETUP PLANE WAVES FOR WAVE FUNCTIONS - number of plane waves = 1048171 - number of sticks = 12469 - - PARALLEL PW FOR CHARGE/POTENTIAL - PROC COLUMNS(POT) PW - 1 3117 262043 - 2 3118 262044 - 3 3117 262043 - 4 3117 262041 - --------------- sum ------------------- - 4 12469 1048171 - - PARALLEL PW FOR WAVE FUNCTIONS - PROC COLUMNS(W) PW - 1 3117 262043 - 2 3118 262044 - 3 3117 262043 - 4 3117 262041 - --------------- sum ------------------- - 4 12469 1048171 - - SETUP COORDINATES OF PLANE WAVES - number of total plane waves = 1048171 + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 64 + nkstot_ibz = 36 + IBZ DirectX DirectY DirectZ Weight ibz2bz + 1 0 0 0 0.015625 0 + 2 -0.25 0 0 0.03125 1 + 3 0.5 0 0 0.015625 2 + 4 0 -0.25 0 0.03125 4 + 5 -0.25 -0.25 0 0.03125 5 + 6 0.5 -0.25 0 0.03125 6 + 7 0.25 -0.25 0 0.03125 7 + 8 0 0.5 0 0.015625 8 + 9 -0.25 0.5 0 0.03125 9 + 10 0.5 0.5 0 0.015625 10 + 11 0 0 -0.25 0.03125 16 + 12 -0.25 0 -0.25 0.03125 17 + 13 0.5 0 -0.25 0.03125 18 + 14 0.25 0 -0.25 0.03125 19 + 15 0 -0.25 -0.25 0.03125 20 + 16 -0.25 -0.25 -0.25 0.03125 21 + 17 0.5 -0.25 -0.25 0.03125 22 + 18 0.25 -0.25 -0.25 0.03125 23 + 19 0 0.5 -0.25 0.03125 24 + 20 -0.25 0.5 -0.25 0.03125 25 + 21 0.5 0.5 -0.25 0.03125 26 + 22 0.25 0.5 -0.25 0.03125 27 + 23 0 0.25 -0.25 0.03125 28 + 24 -0.25 0.25 -0.25 0.03125 29 + 25 0.5 0.25 -0.25 0.03125 30 + 26 0.25 0.25 -0.25 0.03125 31 + 27 0 0 0.5 0.015625 32 + 28 -0.25 0 0.5 0.03125 33 + 29 0.5 0 0.5 0.015625 34 + 30 0 -0.25 0.5 0.03125 36 + 31 -0.25 -0.25 0.5 0.03125 37 + 32 0.5 -0.25 0.5 0.03125 38 + 33 0.25 -0.25 0.5 0.03125 39 + 34 0 0.5 0.5 0.015625 40 + 35 -0.25 0.5 0.5 0.03125 41 + 36 0.5 0.5 0.5 0.015625 42 + nkstot now = 36 - SETUP COORDINATES OF PLANE WAVES - number of |g| = 3309 - max |g| = 5.06505102041 - min |g| = 0 - DONE : INIT PLANEWAVE Time : 1.2043611249 (SEC) + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 0.015625 + 2 -0.25 0 0 0.03125 + 3 0.5 0 0 0.015625 + 4 0 -0.25 0 0.03125 + 5 -0.25 -0.25 0 0.03125 + 6 0.5 -0.25 0 0.03125 + 7 0.25 -0.25 0 0.03125 + 8 0 0.5 0 0.015625 + 9 -0.25 0.5 0 0.03125 + 10 0.5 0.5 0 0.015625 + 11 0 0 -0.25 0.03125 + 12 -0.25 0 -0.25 0.03125 + 13 0.5 0 -0.25 0.03125 + 14 0.25 0 -0.25 0.03125 + 15 0 -0.25 -0.25 0.03125 + 16 -0.25 -0.25 -0.25 0.03125 + 17 0.5 -0.25 -0.25 0.03125 + 18 0.25 -0.25 -0.25 0.03125 + 19 0 0.5 -0.25 0.03125 + 20 -0.25 0.5 -0.25 0.03125 + 21 0.5 0.5 -0.25 0.03125 + 22 0.25 0.5 -0.25 0.03125 + 23 0 0.25 -0.25 0.03125 + 24 -0.25 0.25 -0.25 0.03125 + 25 0.5 0.25 -0.25 0.03125 + 26 0.25 0.25 -0.25 0.03125 + 27 0 0 0.5 0.015625 + 28 -0.25 0 0.5 0.03125 + 29 0.5 0 0.5 0.015625 + 30 0 -0.25 0.5 0.03125 + 31 -0.25 -0.25 0.5 0.03125 + 32 0.5 -0.25 0.5 0.03125 + 33 0.25 -0.25 0.5 0.03125 + 34 0 0.5 0.5 0.015625 + 35 -0.25 0.5 0.5 0.03125 + 36 0.5 0.5 0.5 0.015625 + + k-point number in this process = 36 + minimum distributed K point number = 36 - DONE : INIT CHARGE Time : 1.25489114318 (SEC) + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 0.03125 + 2 -0.028462829115 0 0 0.0625 + 3 0.05692565823 0 0 0.03125 + 4 0 -0.028462829115 0 0.0625 + 5 -0.028462829115 -0.028462829115 0 0.0625 + 6 0.05692565823 -0.028462829115 0 0.0625 + 7 0.028462829115 -0.028462829115 0 0.0625 + 8 0 0.05692565823 0 0.03125 + 9 -0.028462829115 0.05692565823 0 0.0625 + 10 0.0569256582299 0.0569256582299 0 0.03125 + 11 0 0 -0.028462829115 0.0625 + 12 -0.028462829115 0 -0.028462829115 0.0625 + 13 0.05692565823 0 -0.028462829115 0.0625 + 14 0.028462829115 0 -0.028462829115 0.0625 + 15 0 -0.028462829115 -0.028462829115 0.0625 + 16 -0.028462829115 -0.028462829115 -0.028462829115 0.0625 + 17 0.05692565823 -0.028462829115 -0.028462829115 0.0625 + 18 0.028462829115 -0.028462829115 -0.028462829115 0.0625 + 19 0 0.05692565823 -0.028462829115 0.0625 + 20 -0.028462829115 0.05692565823 -0.028462829115 0.0625 + 21 0.05692565823 0.0569256582299 -0.028462829115 0.0625 + 22 0.028462829115 0.05692565823 -0.028462829115 0.0625 + 23 0 0.028462829115 -0.028462829115 0.0625 + 24 -0.028462829115 0.028462829115 -0.028462829115 0.0625 + 25 0.05692565823 0.028462829115 -0.028462829115 0.0625 + 26 0.028462829115 0.028462829115 -0.028462829115 0.0625 + 27 0 0 0.05692565823 0.03125 + 28 -0.028462829115 0 0.05692565823 0.0625 + 29 0.05692565823 0 0.05692565823 0.03125 + 30 0 -0.028462829115 0.05692565823 0.0625 + 31 -0.028462829115 -0.028462829115 0.05692565823 0.0625 + 32 0.05692565823 -0.028462829115 0.05692565823 0.0625 + 33 0.028462829115 -0.028462829115 0.05692565823 0.0625 + 34 0 0.05692565823 0.05692565823 0.03125 + 35 -0.028462829115 0.05692565823 0.05692565823 0.0625 + 36 0.0569256582299 0.0569256582299 0.05692565823 0.03125 - DONE : INIT POTENTIAL Time : 1.26592466421 (SEC) + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 0.03125 + 2 -0.25 0 0 0.0625 + 3 0.5 0 0 0.03125 + 4 0 -0.25 0 0.0625 + 5 -0.25 -0.25 0 0.0625 + 6 0.5 -0.25 0 0.0625 + 7 0.25 -0.25 0 0.0625 + 8 0 0.5 0 0.03125 + 9 -0.25 0.5 0 0.0625 + 10 0.5 0.5 0 0.03125 + 11 0 0 -0.25 0.0625 + 12 -0.25 0 -0.25 0.0625 + 13 0.5 0 -0.25 0.0625 + 14 0.25 0 -0.25 0.0625 + 15 0 -0.25 -0.25 0.0625 + 16 -0.25 -0.25 -0.25 0.0625 + 17 0.5 -0.25 -0.25 0.0625 + 18 0.25 -0.25 -0.25 0.0625 + 19 0 0.5 -0.25 0.0625 + 20 -0.25 0.5 -0.25 0.0625 + 21 0.5 0.5 -0.25 0.0625 + 22 0.25 0.5 -0.25 0.0625 + 23 0 0.25 -0.25 0.0625 + 24 -0.25 0.25 -0.25 0.0625 + 25 0.5 0.25 -0.25 0.0625 + 26 0.25 0.25 -0.25 0.0625 + 27 0 0 0.5 0.03125 + 28 -0.25 0 0.5 0.0625 + 29 0.5 0 0.5 0.03125 + 30 0 -0.25 0.5 0.0625 + 31 -0.25 -0.25 0.5 0.0625 + 32 0.5 -0.25 0.5 0.0625 + 33 0.25 -0.25 0.5 0.0625 + 34 0 0.5 0.5 0.03125 + 35 -0.25 0.5 0.5 0.0625 + 36 0.5 0.5 0.5 0.03125 + DONE : INIT K-POINTS Time : 0.127091526348 (SEC) + + occupied bands = 128 + NLOCAL = 1408 + NBANDS = 154 + NBANDS = 154 + READING ORBITAL FILE NAMES FOR LCAO + orbital file: Si_gga_9au_100Ry_3s3p2d.orb + orbital file: C_gga_9au_100Ry_3s3p2d.orb @@ -279,1913 +535,820 @@ delta r (Bohr) = 0.01 dr_uniform (Bohr) = 0.001 rmax (Bohr) = 30 - kmesh = 711 + kmesh = 1005 ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT - 1 0 0 801 0.01 8 1 1 - 2 0 1 801 0.01 8 1 1 - 3 1 0 801 0.01 8 1 1 + 1 0 0 901 0.01 9 1 1 + 2 0 1 901 0.01 9 1 1 + 3 0 2 901 0.01 9 1 1 + 4 1 0 901 0.01 9 1 1 + 5 1 1 901 0.01 9 1 1 + 6 1 2 901 0.01 9 1 1 + 7 2 0 901 0.01 9 1 1 + 8 2 1 901 0.01 9 1 1 ORBITAL L N nr dr RCUT CHECK_UNIT NEW_UNIT - 1 0 0 701 0.01 7 1 1 - 2 0 1 701 0.01 7 1 1 - 3 1 0 701 0.01 7 1 1 - 4 1 1 701 0.01 7 1 1 - 5 2 0 701 0.01 7 1 1 + 1 0 0 901 0.01 9 1 1 + 2 0 1 901 0.01 9 1 1 + 3 0 2 901 0.01 9 1 1 + 4 1 0 901 0.01 9 1 1 + 5 1 1 901 0.01 9 1 1 + 6 1 2 901 0.01 9 1 1 + 7 2 0 901 0.01 9 1 1 + 8 2 1 901 0.01 9 1 1 SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS SET NONLOCAL PSEUDOPOTENTIAL PROJECTORS max number of nonlocal projetors among all species is 4 SETUP THE TWO-CENTER INTEGRATION TABLES - SETUP THE DIVISION OF H/S MATRIX - divide the H&S matrix using 2D block algorithms. - nb2d = 1 - trace_loc_row dimension = 23 - trace_loc_col dimension = 23 - nloc = 144 - init_chg = atomic - nloc = 144 - searching radius is (Bohr)) = 16.01 - searching radius unit is (Bohr)) = 1 - enter setAlltoallvParameter, nblk = 1 -checkpoint 2 - pnum = 0 - prow = 0 - pcol = 0 - nRow_in_proc = 12 - nCol_in_proc = 12 - pnum = 1 - prow = 0 - pcol = 1 - nRow_in_proc = 12 - nCol_in_proc = 11 - pnum = 2 - prow = 1 - pcol = 0 - nRow_in_proc = 11 - nCol_in_proc = 12 - pnum = 3 - prow = 1 - pcol = 1 - nRow_in_proc = 11 - nCol_in_proc = 11 -receiver_size is 529 ; receiver_size of each process is: -144 132 132 121 -sender_size is 436 ; sender_size of each process is: -144 144 144 4 - gamma_only_local = 1 - - LCAO ALGORITHM ------------- MD = 1 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = 0 - vlocal data are exchanged, received size(M): = 0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = 1 - number of non-zero elements in sender_buffer = 436 - sender_size = 436 - last sender_buffer = 0.000987248 - number of non-zero elements in receiver_buffer = 529 - receiver_size = 529 - last receiver_buffer = 0.000213871 - - Density error is 0.22907025181 - - LCAO ALGORITHM ------------- MD = 1 ELEC = 2 -------------------------------- - -temp variables are deleted - vlocal data are put in sender_buffer, size(M): = 0 - vlocal data are exchanged, received size(M): = 0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = 1 - number of non-zero elements in sender_buffer = 436 - sender_size = 436 - last sender_buffer = 0.00124178 - number of non-zero elements in receiver_buffer = 529 - receiver_size = 529 - last receiver_buffer = 0.000232881 - - Density error is 0.0983063523487 - - LCAO ALGORITHM ------------- MD = 1 ELEC = 3 -------------------------------- - -temp variables are deleted - vlocal data are put in sender_buffer, size(M): = 0 - vlocal data are exchanged, received size(M): = 0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = 1 - number of non-zero elements in sender_buffer = 436 - sender_size = 436 - last sender_buffer = 0.00119187 - number of non-zero elements in receiver_buffer = 529 - receiver_size = 529 - last receiver_buffer = 0.00023854 - - Density error is 0.0630382071563 - - LCAO ALGORITHM ------------- MD = 1 ELEC = 4 -------------------------------- - -temp variables are deleted - vlocal data are put in sender_buffer, size(M): = 0 - vlocal data are exchanged, received size(M): = 0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = 1 - number of non-zero elements in sender_buffer = 436 - sender_size = 436 - last sender_buffer = 0.00111123 - number of non-zero elements in receiver_buffer = 529 - receiver_size = 529 - last receiver_buffer = 0.000247594 - - Density error is 0.00212188907864 + Warning_Memory_Consuming allocated: ORB::Jl(x) 138 MB - charge density convergence is achieved - final etot is -466.692851174 eV + Warning_Memory_Consuming allocated: ORB::Table_SR&TR 52.9 MB - ><><><><><><><><><><><><><><><><><><><><><>< + Warning_Memory_Consuming allocated: ORB::Table_NR 11 MB - TOTAL-FORCE (eV/Angstrom) + SETUP THE DIVISION OF H/S MATRIX + divide the H&S matrix using 2D block algorithms. + nb2d = 64 + parameter nb2d is too large: nb2d = 64 + reset nb2d to value 1, this set would make the program keep working but maybe get slower during diagonalization. + trace_loc_row dimension = 1408 + trace_loc_col dimension = 1408 + nloc = 123904 - ><><><><><><><><><><><><><><><><><><><><><>< + ------------------------------------------- + STEP OF MOLECULAR DYNAMICS : 0 + ------------------------------------------- + searching radius is (Bohr)) = 25.3 + searching radius unit is (Bohr)) = 1.89 +1388640 - atom x y z - H1 +0.86330858 -0.44325497 -0.75698516 - H2 -0.20093087 +0.46812614 -1.160958 - O1 -0.66237771 -0.024871173 +1.9179432 + Warning_Memory_Consuming allocated: pvpR_reduced 84.4 MB + Warning_Memory_Consuming allocated: LOC::DM_R 84.4 MB + init_chg = atomic + DONE : INIT SCF Time : 10.363 (SEC) - ><><><><><><><><><><><><><><><><><><><><><>< - TOTAL-STRESS (KBAR) + LCAO ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Warning_Memory_Consuming allocated: ChgMix::Rrho 5.69531 MB - +0.342474 -0.250612 -0.053956 - -0.250612 +0.199085 -0.098627 - -0.053956 -0.098627 +0.476229 + Density error is 0.271791758684 - ------------------------------------------- - STEP OF MOLECULAR DYNAMICS : 0 - ------------------------------------------- + Energy Rydberg eV + E_KohnSham -613.161307419 -8342.48757402 + E_Harris -621.907629188 -8461.48738663 + E_Fermi +0.661240555023 +8.99663929699 -output Pressure for check! -Virtual Pressure is +0.364728 Kbar -Virial Term is +0.339263 Kbar -Kenetic Term is +0.025466 Kbar - - - ><><><><><><><><><><><><><><><><><><><><><>< - - MD STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.381046 -0.260771 -0.035926 - -0.260771 +0.213637 -0.116654 - -0.035926 -0.116654 +0.499502 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 2 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001111 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000246 - - Density error is +0.000812965099 + LCAO ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- - charge density convergence is achieved - final etot is -466.694119113669 eV + Density error is 0.149449652394 - ><><><><><><><><><><><><><><><><><><><><><>< + Energy Rydberg eV + E_KohnSham -616.884023654 -8393.13772686 + E_Harris -619.644020793 -8430.68941442 + E_Fermi +0.764151461145 +10.3968140066 - TOTAL-FORCE (eV/Angstrom) + LCAO ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 0.022805864506 - atom x y z - H1 +0.64655531 -0.33147708 -0.63237758 - H2 -0.27582922 +0.48531937 -1.07451897 - O1 -0.37072609 -0.15384229 +1.70689655 + Energy Rydberg eV + E_KohnSham -617.840995352 -8406.15799478 + E_Harris -617.842471299 -8406.17807606 + E_Fermi +0.717089159174 +9.75649853879 + LCAO ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 0.000986964092689 - TOTAL-STRESS (KBAR) + Energy Rydberg eV + E_KohnSham -617.842597714 -8406.17979603 + E_Harris -617.84266055 -8406.18065096 + E_Fermi +0.720042173328 +9.79667635757 - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.304825 -0.225915 -0.041597 - -0.225915 +0.184120 -0.109536 - -0.041597 -0.109536 +0.476180 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 3 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001109 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000249 - - Density error is +0.000712200370 + LCAO ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- - charge density convergence is achieved - final etot is -466.695421284274 eV + Density error is 0.000210040595651 - ><><><><><><><><><><><><><><><><><><><><><>< + Energy Rydberg eV + E_KohnSham -617.842621205 -8406.18011564 + E_Harris -617.842619427 -8406.18009145 + E_Fermi +0.720001640421 +9.79612487907 - TOTAL-FORCE (eV/Angstrom) + LCAO ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 2.10063491364e-05 - atom x y z - H1 +0.61896149 -0.29339215 -0.65503589 - H2 -0.21205075 +0.46474918 -1.12721978 - O1 -0.40691074 -0.17135703 +1.78225568 + Energy Rydberg eV + E_KohnSham -617.842621557 -8406.18012044 + E_Harris -617.842621587 -8406.18012084 + E_Fermi +0.720010447555 +9.79624470628 + LCAO ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 2.47068238018e-06 - TOTAL-STRESS (KBAR) + Energy Rydberg eV + E_KohnSham -617.842621568 -8406.18012058 + E_Harris -617.842621568 -8406.18012058 + E_Fermi +0.720014424529 +9.79629881579 - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.270131 -0.203129 -0.030432 - -0.203129 +0.169841 -0.118202 - -0.030432 -0.118202 +0.473338 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 4 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001106 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000249 - - Density error is +0.000693457887 + LCAO ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- - charge density convergence is achieved - final etot is -466.696750196281 eV + Density error is 5.6789597596e-08 - ><><><><><><><><><><><><><><><><><><><><><>< + Energy Rydberg eV + E_KohnSham -617.842621568 -8406.18012058 + E_Harris -617.842621568 -8406.18012058 + E_band +63.4043742298 +862.66076765 + E_one_elec +165.366539162 +2249.92719115 + E_Hartree +75.2834574428 +1024.28398636 + E_xc -193.832170777 -2637.22197828 + E_Ewald -664.660447396 -9043.16931981 + E_demet -2.40480241569e-88 -3.27190154175e-87 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.720014185205 +9.79629555962 - TOTAL-FORCE (eV/Angstrom) + charge density convergence is achieved + final etot is -8406.18012058 eV - ><><><><><><><><><><><><><><><><><><><><><>< + Warning_Memory_Consuming allocated: Force::dS_K 31.7834472656 MB - atom x y z - H1 +0.48644933 -0.21743108 -0.58788434 - H2 -0.24325232 +0.47926564 -1.10488732 - O1 -0.24319701 -0.26183455 +1.69277166 + Warning_Memory_Consuming allocated: Stress::dHr 31.7834472656 MB + Warning_Memory_Consuming allocated: Stress::dSR 63.5668945312 MB - ><><><><><><><><><><><><><><><><><><><><><>< + Warning_Memory_Consuming allocated: Force::dTVNL 31.7834472656 MB - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.232348 -0.178143 -0.019038 - -0.178143 +0.154110 -0.127129 - -0.019038 -0.127129 +0.469916 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 5 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001105 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000251 - - Density error is +0.000831214560 + Warning_Memory_Consuming allocated: Force::edm2d 10.5944824219 MB - charge density convergence is achieved - final etot is -466.698028090263 eV + Warning_Memory_Consuming allocated: Force::dm2d_K 10.5944824219 MB - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< TOTAL-FORCE (eV/Angstrom) - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< atom x y z - H1 +0.40250864 -0.15283133 -0.57921295 - H2 -0.19163250 +0.44793586 -1.10996658 - O1 -0.21087614 -0.29510452 +1.68917953 - - - ><><><><><><><><><><><><><><><><><><><><><>< + Si1 -3.2261899e-07 +8.3498417e-07 +2.986129e-06 + Si2 -3.1218758e-07 +8.6199571e-07 -2.9930621e-06 + Si3 -3.3465795e-07 -8.3573499e-07 +2.9893002e-06 + Si4 -3.1108376e-07 -8.6255082e-07 -2.9807601e-06 + Si5 +3.2549398e-07 +8.2148646e-07 +2.9955983e-06 + Si6 +3.0949044e-07 +8.4434978e-07 -2.9882077e-06 + Si7 +3.34197e-07 -8.18321e-07 +2.9588444e-06 + Si8 +3.1385455e-07 -8.4390684e-07 -2.9646829e-06 + Si9 -2.9439215e-07 -3.9006373e-07 -2.867759e-06 + Si10 -3.0017941e-07 -3.9660488e-07 +2.8675897e-06 + Si11 -3.4843271e-07 +3.9250947e-07 -2.8410243e-06 + Si12 -3.3752987e-07 +3.9487574e-07 +2.8402986e-06 + Si13 +3.0150802e-07 -4.0949763e-07 -2.8355087e-06 + Si14 +2.9547848e-07 -4.3652575e-07 +2.8336029e-06 + Si15 +3.4373307e-07 +4.0444968e-07 -2.8097193e-06 + Si16 +3.423838e-07 +4.3782093e-07 +2.8107147e-06 + Si17 -1.9158775e-06 +8.2679068e-07 -2.8149325e-06 + Si18 -1.9215524e-06 +8.0936979e-07 +2.8135111e-06 + Si19 -1.9045784e-06 -8.2077737e-07 -2.8430482e-06 + Si20 -1.8766384e-06 -8.1434724e-07 +2.8458945e-06 + Si21 +1.9192637e-06 +8.6992761e-07 -2.8270155e-06 + Si22 +1.9179926e-06 +8.5639563e-07 +2.8286972e-06 + Si23 +1.8988585e-06 -8.7379542e-07 -2.8689487e-06 + Si24 +1.8800544e-06 -8.5158207e-07 +2.8641166e-06 + Si25 -1.9122417e-06 -4.2139614e-07 +2.9721926e-06 + Si26 -1.8810948e-06 -3.8887431e-07 -2.976625e-06 + Si27 -1.9295225e-06 +4.1821686e-07 +2.9886028e-06 + Si28 -1.8961859e-06 +3.9056003e-07 -2.9847939e-06 + Si29 +1.9125908e-06 -4.3004337e-07 +2.9783519e-06 + Si30 +1.8780249e-06 -3.927214e-07 -2.9708144e-06 + Si31 +1.9264478e-06 +4.3052262e-07 +2.9907283e-06 + Si32 +1.8991038e-06 +3.906983e-07 -2.9940813e-06 + C1 -1.3144757e-06 +1.0204591e-06 -4.8332547e-06 + C2 -1.3291188e-06 +1.0357242e-06 +4.8287935e-06 + C3 -1.3217428e-06 -1.0222407e-06 -4.8377273e-06 + C4 -1.3144548e-06 -1.0375892e-06 +4.8325182e-06 + C5 +1.3144849e-06 +1.052177e-06 -4.8586575e-06 + C6 +1.3292095e-06 +1.0503198e-06 +4.8534468e-06 + C7 +1.3217829e-06 -1.0539713e-06 -4.8853564e-06 + C8 +1.3144695e-06 -1.0519398e-06 +4.8808406e-06 + C9 -1.3430057e-06 +3.3502914e-07 0 + C10 -1.3334939e-06 +3.3923886e-07 0 + C11 -1.309324e-06 -3.3311415e-07 0 + C12 -1.2940526e-06 -3.3738548e-07 0 + C13 +1.343363e-06 +3.7226725e-07 0 + C14 +1.3331731e-06 +3.9940027e-07 0 + C15 +1.3090982e-06 -3.7032185e-07 0 + C16 +1.2942308e-06 -3.9741179e-07 0 + C17 -1.8915536e-06 +1.024505e-06 0 + C18 -1.8664739e-06 +1.0183317e-06 0 + C19 -1.8545655e-06 -1.0262071e-06 0 + C20 -1.8064329e-06 -1.0198638e-06 0 + C21 +1.891451e-06 +1.0585248e-06 0 + C22 +1.8664858e-06 +1.0573289e-06 0 + C23 +1.8546042e-06 -1.0601434e-06 0 + C24 +1.8065625e-06 -1.0590302e-06 0 + C25 -1.8276796e-06 +3.8537691e-07 -4.8572007e-06 + C26 -1.8586072e-06 +3.4140583e-07 +4.8517596e-06 + C27 -1.8599613e-06 -3.8310089e-07 -4.8626692e-06 + C28 -1.8727778e-06 -3.3983957e-07 +4.8585861e-06 + C29 +1.8279516e-06 +3.9241315e-07 -4.8466914e-06 + C30 +1.8583666e-06 +3.2706382e-07 +4.8423385e-06 + C31 +1.8596494e-06 -3.908495e-07 -4.8484349e-06 + C32 +1.873135e-06 -3.2476766e-07 +4.8429135e-06 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< TOTAL-STRESS (KBAR) - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.192212 -0.150822 -0.009745 - -0.150822 +0.135827 -0.133329 - -0.009745 -0.133329 +0.463055 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 6 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001101 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000252 - - Density error is +0.000741826297 + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< - charge density convergence is achieved - final etot is -466.699290513689 eV + +0.001159 +0.000000 -0.000000 + +0.000000 +0.001159 -0.000000 + -0.000000 -0.000000 +0.001159 + TOTAL-PRESSURE: +0.001159 KBAR - ><><><><><><><><><><><><><><><><><><><><><>< - TOTAL-FORCE (eV/Angstrom) + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -617.84083 -617.84262 +0.0017955843 +3 +0.039668008 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +0.039668008 kbar +Virial Term is +0.0011591866 kbar +Kinetic Term is +0.038508821 kbar - ><><><><><><><><><><><><><><><><><><><><><>< - atom x y z - H1 +0.30844698 -0.10059691 -0.51834944 - H2 -0.21993046 +0.46606276 -1.09553665 - O1 -0.08851653 -0.36546584 +1.61388609 + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + MD STRESS (kbar) - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< - TOTAL-STRESS (KBAR) ++0.037127512 -0.0056934092 -5.7570445e-05 +-0.0056934092 +0.03724801 -0.0079890318 +-5.7570445e-05 -0.0079890318 +0.044628502 - ><><><><><><><><><><><><><><><><><><><><><>< - +0.154744 -0.125715 +0.000150 - -0.125715 +0.119479 -0.140314 - +0.000150 -0.140314 +0.457170 ------------------------------------------- - STEP OF MOLECULAR DYNAMICS : 5 + STEP OF MOLECULAR DYNAMICS : 1 ------------------------------------------- + NEW-OLD atomic charge density approx. for the potential ! + searching radius is (Bohr)) = +25.29 + searching radius unit is (Bohr)) = +1.8897261 ++1388640 + DONE : INIT SCF Time : +481.692 (SEC) -output Pressure for check! -Virtual Pressure is +0.270990 Kbar -Virial Term is +0.243798 Kbar -Kenetic Term is +0.027192 Kbar - - - ><><><><><><><><><><><><><><><><><><><><><>< - - MD STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.197322 -0.137704 +0.012493 - -0.137704 +0.137750 -0.159772 - +0.012493 -0.159772 +0.477896 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 7 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001100 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000254 - - Density error is +0.001296852096 - charge density convergence is achieved - final etot is -466.700352492361 eV + LCAO ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is +0.000291836776751 - TOTAL-FORCE (eV/Angstrom) + Energy Rydberg eV + E_KohnSham -617.842585536 -8406.17963034 + E_Harris -617.842601389 -8406.17984603 + E_Fermi +0.719980033872 +9.79583090689 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 2 ELEC= 2-------------------------------- - atom x y z - H1 +0.18090284 -0.00124347 -0.52452226 - H2 -0.13733836 +0.40367906 -1.08114493 - O1 -0.04356447 -0.40243559 +1.60566719 + Density error is 0.000174536924994 + Energy Rydberg eV + E_KohnSham -617.842584634 -8406.17961806 + E_Harris -617.842599133 -8406.17981534 + E_Fermi +0.719961401319 +9.79557739801 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 2 ELEC= 3-------------------------------- - TOTAL-STRESS (KBAR) + Density error is 0.000146817938021 - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.108237 -0.092885 +0.006743 - -0.092885 +0.096063 -0.142871 - +0.006743 -0.142871 +0.444942 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 8 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001095 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000255 - - Density error is +0.001373100441 + Energy Rydberg eV + E_KohnSham -617.842589754 -8406.17968773 + E_Harris -617.842598504 -8406.17980678 + E_Fermi +0.719957010936 +9.79551766378 - charge density convergence is achieved - final etot is -466.701391168881 eV + LCAO ALGORITHM --------------- ION= 2 ELEC= 4-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 4.01311368176e-05 - TOTAL-FORCE (eV/Angstrom) + Energy Rydberg eV + E_KohnSham -617.842593417 -8406.17973757 + E_Harris -617.842594231 -8406.17974864 + E_Fermi +0.719983315104 +9.79587555035 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 2 ELEC= 5-------------------------------- - atom x y z - H1 +0.14255182 -0.00101230 -0.42624709 - H2 -0.21850033 +0.46069015 -1.06078607 - O1 +0.07594851 -0.45967785 +1.48703316 + Density error is 2.60416512673e-05 + Energy Rydberg eV + E_KohnSham -617.842593752 -8406.17974212 + E_Harris -617.842594082 -8406.17974662 + E_Fermi +0.719982700922 +9.79586719396 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 2 ELEC= 6-------------------------------- - TOTAL-STRESS (KBAR) + Density error is 8.85001150618e-06 - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.076272 -0.071788 +0.016002 - -0.071788 +0.082562 -0.149268 - +0.016002 -0.149268 +0.438978 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 9 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001096 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000256 - - Density error is +0.002916062746 + Energy Rydberg eV + E_KohnSham -617.842593915 -8406.17974434 + E_Harris -617.842593943 -8406.17974472 + E_Fermi +0.719982730732 +9.79586759955 - charge density convergence is achieved - final etot is -466.701752940586 eV + LCAO ALGORITHM --------------- ION= 2 ELEC= 7-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 1.73362166481e-06 - TOTAL-FORCE (eV/Angstrom) + Energy Rydberg eV + E_KohnSham -617.842593926 -8406.1797445 + E_Harris -617.842593927 -8406.17974451 + E_Fermi +0.719983060311 +9.7958720837 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 2 ELEC= 8-------------------------------- - atom x y z - H1 -0.07047054 +0.18417814 -0.50830181 - H2 -0.02028818 +0.30684812 -1.03356989 - O1 +0.09075872 -0.49102625 +1.54187171 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) + Density error is 5.9027453997e-07 - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.016733 -0.027790 +0.017836 - -0.027790 +0.048898 -0.145410 - +0.017836 -0.145410 +0.417656 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 10 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001086 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000258 - - Density error is +0.004281856614 + Energy Rydberg eV + E_KohnSham -617.842593927 -8406.1797445 + E_Harris -617.842593927 -8406.17974451 + E_band +63.4043638131 +862.660625923 + E_one_elec +165.366403961 +2249.92535164 + E_Hartree +75.2835214476 +1024.28485719 + E_xc -193.83217461 -2637.22203043 + E_Ewald -664.660344725 -9043.16792291 + E_demet -2.40480241569e-88 -3.27190154175e-87 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.719982829671 +9.79586894569 charge density convergence is achieved - final etot is -466.701784879168 eV + final etot is -8406.1797445 eV - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< TOTAL-FORCE (eV/Angstrom) - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< atom x y z - H1 +0.03821444 +0.03386400 -0.27622989 - H2 -0.29847686 +0.50989617 -1.00686614 - O1 +0.26026241 -0.54376017 +1.28309603 - - - ><><><><><><><><><><><><><><><><><><><><><>< + Si1 -0.0003849761 -0.0015249699 -0.0037335733 + Si2 -0.0086430543 +0.0033390282 -0.011190411 + Si3 +0.019030976 -0.007593824 +0.0017668788 + Si4 -0.022349467 +0.015327857 -0.0044691377 + Si5 -0.013810136 -0.016732033 +0.0037153411 + Si6 +0.0071154647 -0.0018635192 +0.0042301769 + Si7 +0.0014466585 +0.0066069925 +0.00076403546 + Si8 -0.0080392373 -0.017077273 +0.018592388 + Si9 -0.0025860406 -0.009494221 +0.0073404881 + Si10 -0.0039216402 +0.0024964849 -0.0039135461 + Si11 +0.0035130574 -0.011483783 +0.0058423201 + Si12 -0.0049270999 +0.0063728681 +0.0020481942 + Si13 -0.0059281708 +0.007110934 +0.0075904939 + Si14 +0.00039268709 -0.0069315421 +0.018259224 + Si15 +0.0057393694 +0.0047936901 +0.016699737 + Si16 -0.0029468718 +0.0040592014 -0.0035384289 + Si17 +0.012932361 -0.018605767 +0.0036656012 + Si18 +0.00058695593 -0.00034743959 -0.0067768452 + Si19 +0.0022241194 -0.013580201 +0.0063457598 + Si20 -0.0023666693 -0.010964168 +0.0056237545 + Si21 +0.001693671 +0.0017169618 -0.0043269683 + Si22 -0.011947793 -0.01510261 +0.014406775 + Si23 +0.0042008394 +0.011215335 +0.01121635 + Si24 -0.0058155212 -0.0061937825 +0.0094468858 + Si25 +0.0055837439 -0.018856085 +0.0084438928 + Si26 +0.0025849103 +0.0020168209 -0.010087135 + Si27 -0.0016716978 -0.0019167937 -0.016157899 + Si28 +0.023365493 -0.019927373 +0.010305371 + Si29 -0.008101632 +0.011054873 +0.0021432679 + Si30 +0.0081319024 -0.0065055415 +0.021167142 + Si31 +0.0092393509 +0.01001467 -0.010019662 + Si32 +0.017024241 +0.0050841453 -0.012978221 + C1 -0.01322085 +0.015811097 -0.013245086 + C2 +0.00560333 +0.0071889978 +0.011837668 + C3 -0.0033287312 +0.016025823 +0.0079656384 + C4 -0.0080406591 +0.0070638159 -0.0057980355 + C5 +0.0057871162 -0.0049395032 +0.0085034688 + C6 +0.0050664214 +0.0083101017 +0.012680041 + C7 -0.00079519551 -0.010869177 -0.0013581146 + C8 -0.0020642803 -0.0079052825 -0.011083794 + C9 +0.0015253946 +0.017396085 +0.0034385485 + C10 -0.012957858 -0.0060670231 -0.014239506 + C11 -0.0068468143 +0.0095816332 +0.012142784 + C12 +0.010664396 +0.023823008 -0.014571057 + C13 -0.016467226 +0.011973208 -0.0017164146 + C14 +0.0080514524 -0.0066638528 -0.014452149 + C15 -0.0031774577 -0.010629531 -0.017454765 + C16 -0.0071708359 -0.0044347788 +0.0022163403 + C17 -0.022301807 +0.01038189 +0.003864238 + C18 -0.0018850142 -0.014550126 +0.010512149 + C19 -0.0031314205 +0.0097696181 -0.016230402 + C20 +0.013762629 +0.0092369217 +0.012163472 + C21 +0.0099977996 -0.0082718533 +0.013384151 + C22 -0.0078986982 -0.0010362825 +0.00056850493 + C23 +0.017884386 -0.0096028459 -0.0052518164 + C24 +0.009638309 +0.010440114 -0.028539597 + C25 +0.002751646 +0.0048650319 +0.0095042438 + C26 -0.008940651 +0.016426318 -0.012337044 + C27 -0.00069785018 +0.0057521995 -0.03014497 + C28 -0.00061592002 +0.0054041328 +0.018746914 + C29 -0.0096415047 +0.0064616293 -0.0043063433 + C30 +0.015095067 +0.011008838 -0.016567886 + C31 -0.015318903 -0.013532055 -0.00078116738 + C32 +0.017307936 -0.01492709 -0.011872264 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< TOTAL-STRESS (KBAR) - ><><><><><><><><><><><><><><><><><><><><><>< - - +0.005309 -0.022976 +0.029731 - -0.022976 +0.048804 -0.155863 - +0.029731 -0.155863 +0.418836 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 11 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001095 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000259 - - Density error is +0.008284286772 + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< - charge density convergence is achieved - final etot is -466.698298260896 eV + +0.002490 +0.087437 -0.088607 + +0.087437 +0.002542 +0.020122 + -0.088607 +0.020122 +0.002267 + TOTAL-PRESSURE: +0.002433 KBAR - ><><><><><><><><><><><><><><><><><><><><><>< - TOTAL-FORCE (eV/Angstrom) + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -617.84034 -617.84259 +0.002256563 +3.7701871 +0.050828452 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +0.050828452 kbar +Virial Term is +0.0024332983 kbar +Kinetic Term is +0.048395154 kbar - ><><><><><><><><><><><><><><><><><><><><><>< - atom x y z - H1 -0.42153194 +0.47800345 -0.60266923 - H2 +0.26521496 +0.07640708 -0.96382431 - O1 +0.15631698 -0.55441053 +1.56649354 + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + MD STRESS (kbar) - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< - TOTAL-STRESS (KBAR) ++0.047748654 +0.080288157 -0.088670434 ++0.080288157 +0.047884483 +0.010099869 +-0.088670434 +0.010099869 +0.05685222 - ><><><><><><><><><><><><><><><><><><><><><>< - -0.091192 +0.052077 +0.020743 - +0.052077 -0.012621 -0.137197 - +0.020743 -0.137197 +0.376312 ------------------------------------------- - STEP OF MOLECULAR DYNAMICS : 10 + STEP OF MOLECULAR DYNAMICS : 2 ------------------------------------------- + first order charge density extrapolation ! + searching radius is (Bohr)) = +25.29 + searching radius unit is (Bohr)) = +1.8897261 ++1388640 + DONE : INIT SCF Time : +955.388 (SEC) -output Pressure for check! -Virtual Pressure is +0.118981 Kbar -Virial Term is +0.090833 Kbar -Kenetic Term is +0.028148 Kbar - - - ><><><><><><><><><><><><><><><><><><><><><>< - - MD STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.049247 +0.041841 +0.026216 - +0.041841 +0.006782 -0.157984 - +0.026216 -0.157984 +0.399408 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 12 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001068 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000260 - - Density error is +0.013857092147 - - LCAO ALGORITHM ------------- MD = 12 ELEC = 2 -------------------------------- - -temp variables are deleted - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001085 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000261 - - Density error is +0.001589448966 - - charge density convergence is achieved - final etot is -466.703909676999 eV - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - H1 -0.28674705 +0.32257779 -0.39663257 - H2 +0.02955609 +0.25720918 -0.94465129 - O1 +0.25719096 -0.57978697 +1.34128386 + LCAO ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is +7.40211564819e-05 - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.102767 +0.057764 +0.030039 - +0.057764 -0.014383 -0.144341 - +0.030039 -0.144341 +0.373965 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 13 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001077 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000262 - - Density error is +0.002070240779 + Energy Rydberg eV + E_KohnSham -617.842483775 -8406.17824581 + E_Harris -617.842484742 -8406.17825898 + E_Fermi +0.719943629798 +9.79533560406 - charge density convergence is achieved - final etot is -466.704036345606 eV + LCAO ALGORITHM --------------- ION= 3 ELEC= 2-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 4.25115089997e-05 - TOTAL-FORCE (eV/Angstrom) + Energy Rydberg eV + E_KohnSham -617.842483747 -8406.17824544 + E_Harris -617.842484582 -8406.17825679 + E_Fermi +0.719941612732 +9.79530816046 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 3 ELEC= 3-------------------------------- - atom x y z - H1 -0.32428699 +0.29359387 -0.24641838 - H2 -0.12773856 +0.34751550 -0.88532823 - O1 +0.45202555 -0.64110937 +1.13174660 + Density error is 3.59946649699e-05 + Energy Rydberg eV + E_KohnSham -617.842484025 -8406.17824921 + E_Harris -617.842484553 -8406.1782564 + E_Fermi +0.719939962885 +9.79528571315 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 3 ELEC= 4-------------------------------- - TOTAL-STRESS (KBAR) + Density error is 1.03918923214e-05 - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.129688 +0.076052 +0.035709 - +0.076052 -0.026981 -0.146605 - +0.035709 -0.146605 +0.363477 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 14 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001080 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000264 - - Density error is +0.004359931704 + Energy Rydberg eV + E_KohnSham -617.842484249 -8406.17825226 + E_Harris -617.842484303 -8406.178253 + E_Fermi +0.719942518609 +9.79532048556 - charge density convergence is achieved - final etot is -466.702852817573 eV + LCAO ALGORITHM --------------- ION= 3 ELEC= 5-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 6.45415585652e-06 - TOTAL-FORCE (eV/Angstrom) + Energy Rydberg eV + E_KohnSham -617.842484272 -8406.17825257 + E_Harris -617.842484292 -8406.17825285 + E_Fermi +0.719942249784 +9.795316828 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 3 ELEC= 6-------------------------------- - atom x y z - H1 -0.55904989 +0.52796169 -0.41105586 - H2 +0.19505420 +0.09971169 -0.84000299 - O1 +0.36399569 -0.62767338 +1.25105885 + Density error is 2.21840137491e-06 + Energy Rydberg eV + E_KohnSham -617.842484282 -8406.17825271 + E_Harris -617.842484284 -8406.17825273 + E_Fermi +0.719942201824 +9.79531617547 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 3 ELEC= 7-------------------------------- - TOTAL-STRESS (KBAR) + Density error is 4.55339184509e-07 - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.195852 +0.127521 +0.029560 - +0.127521 -0.069558 -0.132591 - +0.029560 -0.132591 +0.330830 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 15 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001065 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000265 - - Density error is +0.006891676295 + Energy Rydberg eV + E_KohnSham -617.842484283 -8406.17825272 + E_Harris -617.842484283 -8406.17825272 + E_band +63.4043150279 +862.659962166 + E_one_elec +165.365848386 +2249.91779265 + E_Hartree +75.2837859485 +1024.28845591 + E_xc -193.832191986 -2637.22226684 + E_Ewald -664.659926631 -9043.16223444 + E_demet -2.40480241569e-88 -3.27190154175e-87 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.719942314329 +9.79531770619 charge density convergence is achieved - final etot is -466.700543051512 eV + final etot is -8406.17825272 eV - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< TOTAL-FORCE (eV/Angstrom) - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< atom x y z - H1 -0.34568768 +0.25462803 -0.05926056 - H2 -0.26550846 +0.43144795 -0.80103265 - O1 +0.61119614 -0.68607598 +0.86029320 - - - ><><><><><><><><><><><><><><><><><><><><><>< + Si1 -0.00095048209 -0.0035383106 -0.0086361923 + Si2 -0.019534218 +0.0078056989 -0.025322382 + Si3 +0.043264648 -0.016914788 +0.0041714452 + Si4 -0.050714801 +0.034695636 -0.010429535 + Si5 -0.030974776 -0.038401312 +0.0083364798 + Si6 +0.015534372 -0.0034911726 +0.0094698937 + Si7 +0.0032539497 +0.015297796 +0.0014098024 + Si8 -0.017994154 -0.039124397 +0.04206844 + Si9 -0.0065137669 -0.021722143 +0.016587609 + Si10 -0.0086254826 +0.005793098 -0.0090886748 + Si11 +0.0082065609 -0.025751607 +0.013520131 + Si12 -0.011214201 +0.014415885 +0.004300943 + Si13 -0.01280647 +0.016116292 +0.016102751 + Si14 +0.00072078274 -0.015403701 +0.041927067 + Si15 +0.012465002 +0.010785289 +0.037929953 + Si16 -0.0065440693 +0.0093774158 -0.0082847813 + Si17 +0.029267325 -0.041488269 +0.0082071788 + Si18 +0.0015761654 -0.00079309335 -0.015463042 + Si19 +0.0047430271 -0.030663452 +0.013908507 + Si20 -0.0053657591 -0.024901793 +0.012915089 + Si21 +0.0037232282 +0.003319293 -0.0098828108 + Si22 -0.026968046 -0.033839078 +0.032744378 + Si23 +0.0098547366 +0.025869496 +0.02560142 + Si24 -0.013488478 -0.01436203 +0.021016101 + Si25 +0.012895019 -0.04240366 +0.018786249 + Si26 +0.0053840778 +0.004800503 -0.022609317 + Si27 -0.0036819556 -0.004080584 -0.036304645 + Si28 +0.052655055 -0.045150405 +0.022989489 + Si29 -0.018830387 +0.025210817 +0.0051574582 + Si30 +0.018954503 -0.01488157 +0.047105913 + Si31 +0.020707525 +0.022457776 -0.023259265 + Si32 +0.038630764 +0.011651561 -0.029013674 + C1 -0.029799565 +0.035670115 -0.02897721 + C2 +0.01273808 +0.015830928 +0.026195765 + C3 -0.007275111 +0.035459741 +0.017033032 + C4 -0.017568727 +0.016259495 -0.01241047 + C5 +0.01333647 -0.011046717 +0.019781618 + C6 +0.011009554 +0.0186559 +0.02771181 + C7 -0.0016765722 -0.024409429 -0.0034818133 + C8 -0.0047315554 -0.017566626 -0.02456004 + C9 +0.0044236546 +0.038807027 +0.0067993569 + C10 -0.029287468 -0.01290273 -0.030799373 + C11 -0.015882368 +0.021679116 +0.026739998 + C12 +0.024261134 +0.052423154 -0.032584164 + C13 -0.037062518 +0.025573661 -0.0033013372 + C14 +0.018474714 -0.014714167 -0.032454279 + C15 -0.0066438964 -0.022890122 -0.03865958 + C16 -0.016417945 -0.010140873 +0.0045340588 + C17 -0.049102821 +0.023758988 +0.008926594 + C18 -0.0039919878 -0.032462783 +0.023081896 + C19 -0.0069900893 +0.021484908 -0.036263843 + C20 +0.030151933 +0.020627044 +0.027067176 + C21 +0.021869347 -0.019675919 +0.029431207 + C22 -0.017839481 -0.0014851615 +0.0015963314 + C23 +0.039427399 -0.020271883 -0.011839624 + C24 +0.021617717 +0.022397017 -0.062912985 + C25 +0.0055340934 +0.011065086 +0.021524229 + C26 -0.019290817 +0.036231383 -0.027788838 + C27 -0.0015048067 +0.012564059 -0.067047343 + C28 -0.001139323 +0.012246798 +0.04165354 + C29 -0.021168499 +0.014216436 -0.010893603 + C30 +0.033096099 +0.02461893 -0.035966521 + C31 -0.034072527 -0.029861021 -0.0011538188 + C32 +0.037876187 -0.032827543 -0.026943746 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< TOTAL-STRESS (KBAR) - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.187581 +0.117448 +0.041239 - +0.117448 -0.058254 -0.143489 - +0.041239 -0.143489 +0.334349 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 16 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001081 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000268 - - Density error is +0.013146435036 - - LCAO ALGORITHM ------------- MD = 16 ELEC = 2 -------------------------------- - -temp variables are deleted - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001066 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000268 - - Density error is +0.001586984246 + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< - charge density convergence is achieved - final etot is -466.703646638347 eV + +0.007954 +0.195968 -0.199596 + +0.195968 +0.008227 +0.044672 + -0.199596 +0.044672 +0.006841 + TOTAL-PRESSURE: +0.007674 KBAR - ><><><><><><><><><><><><><><><><><><><><><>< - TOTAL-FORCE (eV/Angstrom) + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -617.83797 -617.84248 +0.0045123743 +7.5391184 +0.10444823 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +0.10444823 kbar +Virial Term is +0.0076740417 kbar +Kinetic Term is +0.096774188 kbar - ><><><><><><><><><><><><><><><><><><><><><>< - atom x y z - H1 -0.54319860 +0.45716115 -0.20682151 - H2 +0.02270964 +0.21154904 -0.75898021 - O1 +0.52048896 -0.66871019 +0.96580172 + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + MD STRESS (kbar) - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< - TOTAL-STRESS (KBAR) ++0.098734491 +0.1817043 -0.19967246 ++0.1817043 +0.098838512 +0.024734866 +-0.19967246 +0.024734866 +0.11577169 - ><><><><><><><><><><><><><><><><><><><><><>< - -0.247918 +0.164911 +0.034034 - +0.164911 -0.098300 -0.128317 - +0.034034 -0.128317 +0.301503 ------------------------------------------- - STEP OF MOLECULAR DYNAMICS : 15 + STEP OF MOLECULAR DYNAMICS : 3 ------------------------------------------- + second order charge density extrapolation ! + alpha = +4.1830328 + beta = -3.2599046 + searching radius is (Bohr)) = +25.29 + searching radius unit is (Bohr)) = +1.8897261 ++1388640 + DONE : INIT SCF Time : +1376.48 (SEC) -output Pressure for check! -Virtual Pressure is +0.012883 Kbar -Virial Term is -0.014905 Kbar -Kenetic Term is +0.027788 Kbar - - - ><><><><><><><><><><><><><><><><><><><><><>< - - MD STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.210636 +0.159462 +0.032546 - +0.159462 -0.080357 -0.150043 - +0.032546 -0.150043 +0.329644 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 17 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001067 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000269 - - Density error is +0.003632561369 - - charge density convergence is achieved - final etot is -466.702235890628 eV - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - H1 -0.80094970 +0.67278361 -0.30718791 - H2 +0.24366564 +0.00932187 -0.67175682 - O1 +0.55728406 -0.68210548 +0.97894473 - - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.307521 +0.211953 +0.026554 - +0.211953 -0.138106 -0.113019 - +0.026554 -0.113019 +0.268271 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 18 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001054 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000271 - - Density error is +0.005595449442 - - charge density convergence is achieved - final etot is -466.700163595798 eV - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) - - ><><><><><><><><><><><><><><><><><><><><><>< - - atom x y z - H1 -0.59763214 +0.43904849 -0.03472448 - H2 -0.09248416 +0.25763720 -0.63673302 - O1 +0.69011630 -0.69668569 +0.67145750 + LCAO ALGORITHM --------------- ION=+4 ELEC=+1 -------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) + Density error is +1.5440461629e-05 - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.303840 +0.206886 +0.033204 - +0.206886 -0.132651 -0.117370 - +0.033204 -0.117370 +0.264195 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 19 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001066 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000273 - - Density error is +0.010881139789 - - LCAO ALGORITHM ------------- MD = 19 ELEC = 2 -------------------------------- - -temp variables are deleted - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001054 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000273 - - Density error is +0.001371997750 + Energy Rydberg eV + E_KohnSham -617.84214824 -8406.17368063 + E_Harris -617.842148378 -8406.17368251 + E_Fermi +0.719872775575 +9.79437158289 - charge density convergence is achieved - final etot is -466.701537327762 eV + LCAO ALGORITHM --------------- ION= 4 ELEC= 2-------------------------------- - ><><><><><><><><><><><><><><><><><><><><><>< + Density error is 2.2435404381e-05 - TOTAL-FORCE (eV/Angstrom) + Energy Rydberg eV + E_KohnSham -617.842148265 -8406.17368096 + E_Harris -617.842148431 -8406.17368322 + E_Fermi +0.719877599289 +9.79443721289 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 4 ELEC= 3-------------------------------- - atom x y z - H1 -0.77301593 +0.61134487 -0.14930516 - H2 +0.13253222 +0.07664781 -0.58340174 - O1 +0.64048370 -0.68799268 +0.73270691 + Density error is 2.11160311253e-06 + Energy Rydberg eV + E_KohnSham -617.842148335 -8406.17368191 + E_Harris -617.842148336 -8406.17368193 + E_Fermi +0.719874771253 +9.79439873548 - ><><><><><><><><><><><><><><><><><><><><><>< + LCAO ALGORITHM --------------- ION= 4 ELEC= 4-------------------------------- - TOTAL-STRESS (KBAR) + Density error is 5.67267276719e-07 - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.355835 +0.248594 +0.024707 - +0.248594 -0.169021 -0.100853 - +0.024707 -0.100853 +0.231354 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 20 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001054 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000275 - - Density error is +0.003244323553 + Energy Rydberg eV + E_KohnSham -617.842148335 -8406.17368192 + E_Harris -617.842148335 -8406.17368192 + E_band +63.404168539 +862.657969083 + E_one_elec +165.364087504 +2249.89383463 + E_Hartree +75.2846276719 +1024.29990815 + E_xc -193.832253227 -2637.22310007 + E_Ewald -664.658610284 -9043.14432463 + E_demet -2.40480241569e-88 -3.27190154175e-87 + E_descf +0 +0 + E_exx +0 +0 + E_Fermi +0.71987477658 +9.79439880796 charge density convergence is achieved - final etot is -466.699800890155 eV + final etot is -8406.17368192 eV - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< TOTAL-FORCE (eV/Angstrom) - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< atom x y z - H1 -0.98747030 +0.79286130 -0.23966801 - H2 +0.33571389 -0.11433771 -0.49025776 - O1 +0.65175640 -0.67852359 +0.72992577 - - - ><><><><><><><><><><><><><><><><><><><><><>< + Si1 -0.0018979543 -0.006191127 -0.016497161 + Si2 -0.037019015 +0.014800347 -0.048161978 + Si3 +0.08157404 -0.031756173 +0.0073496854 + Si4 -0.095227059 +0.065944038 -0.019662277 + Si5 -0.058118615 -0.072100336 +0.015958621 + Si6 +0.028873559 -0.006478226 +0.017401551 + Si7 +0.0064907358 +0.028464562 +0.0020933595 + Si8 -0.034502948 -0.073269963 +0.079208915 + Si9 -0.012263813 -0.040495538 +0.030667923 + Si10 -0.016373133 +0.01096696 -0.017255235 + Si11 +0.015013581 -0.048686975 +0.024568206 + Si12 -0.021102393 +0.027611629 +0.0088237771 + Si13 -0.024213619 +0.030360434 +0.03035839 + Si14 +0.0013812186 -0.029073595 +0.078050476 + Si15 +0.023756439 +0.020779859 +0.071117014 + Si16 -0.012394501 +0.018171603 -0.015850737 + Si17 +0.054776129 -0.077995818 +0.014770595 + Si18 +0.0034589003 -0.0014523965 -0.029135113 + Si19 +0.0091797637 -0.056908776 +0.025875935 + Si20 -0.010286339 -0.046877919 +0.024550031 + Si21 +0.0066257396 +0.0067580161 -0.018802898 + Si22 -0.050661437 -0.063921043 +0.061714737 + Si23 +0.018535407 +0.04785414 +0.047798612 + Si24 -0.026007386 -0.026651991 +0.039476615 + Si25 +0.023761165 -0.079334245 +0.034927336 + Si26 +0.010584794 +0.0090750346 -0.042982967 + Si27 -0.0070319219 -0.0074272762 -0.068222909 + Si28 +0.099099352 -0.08453164 +0.042760181 + Si29 -0.035205874 +0.047557482 +0.0087836368 + Si30 +0.035206816 -0.027629223 +0.088911692 + Si31 +0.039160705 +0.0423321 -0.043923686 + Si32 +0.072674017 +0.021746478 -0.055151652 + C1 -0.053689424 +0.065704327 -0.052876209 + C2 +0.023040639 +0.029456392 +0.04807079 + C3 -0.013417106 +0.065437173 +0.031277376 + C4 -0.032548547 +0.030290078 -0.023352492 + C5 +0.024393319 -0.020286783 +0.03646852 + C6 +0.02043022 +0.03495585 +0.051853164 + C7 -0.0031450603 -0.045590345 -0.0065690084 + C8 -0.0090437851 -0.032310217 -0.04512665 + C9 +0.0079603814 +0.072323521 +0.012305044 + C10 -0.053093696 -0.024223459 -0.056230704 + C11 -0.029067028 +0.039985758 +0.048459861 + C12 +0.045055498 +0.096800026 -0.060155599 + C13 -0.066486369 +0.046183935 -0.0061575827 + C14 +0.033068169 -0.027487536 -0.059149285 + C15 -0.013101248 -0.041736476 -0.07170382 + C16 -0.03063955 -0.018508293 +0.0085580141 + C17 -0.089883797 +0.044237858 +0.015917238 + C18 -0.0070985765 -0.059699756 +0.042688549 + C19 -0.012009911 +0.039429291 -0.067289559 + C20 +0.055595772 +0.037627863 +0.049511812 + C21 +0.040216328 -0.036093085 +0.053842542 + C22 -0.033601085 -0.0030000276 +0.0030183711 + C23 +0.071098555 -0.037488781 -0.022148017 + C24 +0.039314698 +0.041652896 -0.11450041 + C25 +0.010885038 +0.02037587 +0.039628976 + C26 -0.034974039 +0.065872163 -0.050356217 + C27 -0.0018467171 +0.023286929 -0.12276412 + C28 -0.0021994982 +0.023174227 +0.075358089 + C29 -0.039811787 +0.026257253 -0.020022559 + C30 +0.061270926 +0.045423003 -0.066369593 + C31 -0.063191095 -0.054579082 -0.0035743931 + C32 +0.068672422 -0.059110993 -0.0481328 + + + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< TOTAL-STRESS (KBAR) - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.407715 +0.290577 +0.015274 - +0.290577 -0.205965 -0.083362 - +0.015274 -0.083362 +0.197294 - nloc = +144 - searching radius is (Bohr)) = +16.010000 - searching radius unit is (Bohr)) = +1.000000 - enter setAlltoallvParameter, nblk = +1 -checkpoint 2 - pnum = +0 - prow = +0 - pcol = +0 - nRow_in_proc = +12 - nCol_in_proc = +12 - pnum = +1 - prow = +0 - pcol = +1 - nRow_in_proc = +12 - nCol_in_proc = +11 - pnum = +2 - prow = +1 - pcol = +0 - nRow_in_proc = +11 - nCol_in_proc = +12 - pnum = +3 - prow = +1 - pcol = +1 - nRow_in_proc = +11 - nCol_in_proc = +11 -receiver_size is +529 ; receiver_size of each process is: -+144 +132 +132 +121 -sender_size is +436 ; sender_size of each process is: -+144 +144 +144 +4 - gamma_only_local = +1 - - LCAO ALGORITHM ------------- MD = 21 ELEC = 1 -------------------------------- - -temp variables are deleted - -vlocal exchange index is built - buffer size(M): = 0 - buffer index size(M): = 0 - vlocal data are put in sender_buffer, size(M): = +0 - vlocal data are exchanged, received size(M): = +0 - start solver, ks_solver = genelpa - -K-S equation was solved by genelpa2 - -eigenvalues were copied to ekb - cal_dk_gamma_from_2D, NSPIN = +1 - number of non-zero elements in sender_buffer = +436 - sender_size = +436 - last sender_buffer = +0.001042 - number of non-zero elements in receiver_buffer = +529 - receiver_size = +529 - last receiver_buffer = +0.000277 - - Density error is +0.004953382147 - - charge density convergence is achieved - final etot is -466.697608297566 eV - - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-FORCE (eV/Angstrom) + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< - ><><><><><><><><><><><><><><><><><><><><><>< + +0.025289 +0.365191 -0.374927 + +0.365191 +0.026275 +0.081979 + -0.374927 +0.081979 +0.021407 + TOTAL-PRESSURE: +0.024324 KBAR - atom x y z - H1 -0.81232991 +0.58791846 +0.00094132 - H2 +0.03982643 +0.10078573 -0.45016602 - O1 +0.77250348 -0.68870419 +0.44922470 + ------------------------------------------------------------------------------------------------ + Energy (Ry) Potential (Ry) Kinetic (Ry) Temperature (K) Pressure (kbar) + -617.82763 -617.84215 +0.014517254 +24.254924 +0.33566692 + ------------------------------------------------------------------------------------------------ +Virtual Pressure is +0.33566692 kbar +Virial Term is +0.024324075 kbar +Kinetic Term is +0.31134285 kbar - ><><><><><><><><><><><><><><><><><><><><><>< - - TOTAL-STRESS (KBAR) - - ><><><><><><><><><><><><><><><><><><><><><>< - - -0.404278 +0.286671 +0.018904 - +0.286671 -0.202682 -0.083866 - +0.018904 -0.083866 +0.189109 - - ------------------------------------------- - STEP OF MOLECULAR DYNAMICS : 20 - ------------------------------------------- -output Pressure for check! -Virtual Pressure is -0.113167 Kbar -Virial Term is -0.139283 Kbar -Kenetic Term is +0.026116 Kbar + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< + MD STRESS (kbar) - ><><><><><><><><><><><><><><><><><><><><><>< + ><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>< - MD STRESS (KBAR) ++0.31847067 +0.31941546 -0.37495225 ++0.31941546 +0.31752808 +0.018316838 +-0.37495225 +0.018316838 +0.37100202 - ><><><><><><><><><><><><><><><><><><><><><>< - -0.373570 +0.287440 +0.010819 - +0.287440 -0.188168 -0.105266 - +0.010819 -0.105266 +0.222236 -------------------------------------------- - !FINAL_ETOT_IS -466.6976082975657505 eV + !FINAL_ETOT_IS -8406.173681919036 eV -------------------------------------------- @@ -2194,91 +1357,128 @@ Kenetic Term is +0.026116 Kbar |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- - total +132.35550 11 +12.03 +100.00% - Run_lcao lcao_line +132.33977 1 +132.34 +99.99% - PW_Basis gen_pw +1.16916 1 +1.17 +0.88% - PW_complement get_total_pw +0.11398 10 +0.01 +0.09% - PW_complement setup_GVectors +0.25635 10 +0.03 +0.19% - mymath heapsort +0.20875 10 +0.02 +0.16% - PW_Basis setup_struc_factor +0.47204 21 +0.02 +0.36% - ORB_control read_orb_first +0.12504 1 +0.13 +0.09% - LCAO_Orbitals Read_Orbitals +0.12504 1 +0.13 +0.09% - ORB_control set_orb_tables +1.21148 1 +1.21 +0.92% - ORB_gen_tables gen_tables +1.21148 1 +1.21 +0.92% - ORB_table_phi init_Table +0.71243 1 +0.71 +0.54% - ORB_table_phi cal_ST_Phi12_R +0.70420 126 +0.01 +0.53% - ORB_table_beta init_Table_Beta +0.30461 1 +0.30 +0.23% - ORB_table_beta VNL_PhiBeta_R +0.30229 56 +0.01 +0.23% - Potential init_pot +24.59861 42 +0.59 +18.59% - Potential set_local_pot +1.80187 42 +0.04 +1.36% - FFT FFT3D +39.89220 1316 +0.03 +30.14% - Charge atomic_rho +3.11639 41 +0.08 +2.35% - Potential v_of_rho +36.45681 69 +0.53 +27.54% - XC_Functional v_xc +39.40750 90 +0.44 +29.77% - H_Hartree_pw v_hartree +5.69526 69 +0.08 +4.30% - Potential set_vr_eff +0.22940 69 +0.00 +0.17% - Run_MD_LCAO opt_ions +128.93060 1 +128.93 +97.41% - NVT_NHC setup +8.70219 1 +8.70 +6.57% - MD_func force_stress +63.15373 11 +5.74 +47.72% - LOOP_elec solve_elec_stru +30.69312 21 +1.46 +23.19% - LOOP_elec set_matrix_grid +1.76637 21 +0.08 +1.33% - Grid_Technique init +1.76335 21 +0.08 +1.33% - Grid_BigCellgrid_expansion_index +1.39932 42 +0.03 +1.06% - LOOP_elec solver +28.90742 21 +1.38 +21.84% - ELEC_scf scf +28.90729 21 +1.38 +21.84% - H_Ewald_pw compute_ewald +0.21927 21 +0.01 +0.17% - ELEC_cband_gamma cal_bands +5.01029 27 +0.19 +3.79% - LCAO_Hamilt cal_Hgamma +4.88214 27 +0.18 +3.69% - Gint_Gamma cal_vlocal +4.88196 27 +0.18 +3.69% - Gint_Gamma gamma_vlocal +3.34387 27 +0.12 +2.53% - Local_Orbital_Cha sum_bands +6.29288 27 +0.23 +4.75% - Gint_Gamma cal_rho +6.22736 27 +0.23 +4.71% - Gint_Gamma gamma_charge +6.22723 27 +0.23 +4.70% - Gint_Gamma reduce_charge +1.93070 27 +0.07 +1.46% - Charge mix_rho +2.62751 27 +0.10 +1.99% - Force_Stress_LCAO getForceStress +82.70782 21 +3.94 +62.49% - Forces cal_force_loc +1.64530 21 +0.08 +1.24% - Forces cal_force_ew +0.76779 21 +0.04 +0.58% - Stress_Func stress_loc +2.86125 21 +0.14 +2.16% - Stress_Func stress_har +2.01964 21 +0.10 +1.53% - Stress_Func stress_ew +1.07900 21 +0.05 +0.82% - Stress_Func stress_gga +4.78231 21 +0.23 +3.61% - Force_LCAO_gamma ftable_gamma +56.46509 21 +2.69 +42.66% - Force_LCAO_gamma cal_fvl_dphi +56.40976 21 +2.69 +42.62% - Gint_Gamma cal_force +44.33796 21 +2.11 +33.50% - Gint_Gamma gamma_force +26.79047 21 +1.28 +20.24% - Gint_Gamma gamma_force_wait +17.53623 21 +0.84 +13.25% - MD_func md_force_stress +60.66036 11 +5.51 +45.83% + total +1639.2 13 +1.3e+02 +1e+02 % + Driver driver_line +1639.1 1 +1.6e+03 +1e+02 % + PW_Basis setup_struc_factor +0.3451 4 +0.086 +0.021 % + ORB_control read_orb_first +0.20953 1 +0.21 +0.013 % + LCAO_Orbitals Read_Orbitals +0.20948 1 +0.21 +0.013 % + NOrbital_Lm extra_uniform +0.10349 16 +0.0065 +0.0063 % + ORB_control set_orb_tables +8.562 1 +8.6 +0.52 % + ORB_gen_tables gen_tables +8.562 1 +8.6 +0.52 % + ORB_table_phi init_Table +6.5453 1 +6.5 +0.4 % + ORB_table_phi cal_ST_Phi12_R +6.5012 558 +0.012 +0.4 % + ORB_table_beta init_Table_Beta +1.5347 1 +1.5 +0.094 % + ORB_table_beta VNL_PhiBeta_R +1.5249 168 +0.0091 +0.093 % + Run_MD md_line +1630.1 1 +1.6e+03 +99 % + Nose_Hoover setup +471.93 1 +4.7e+02 +29 % + MD_func force_virial +1630 4 +4.1e+02 +99 % + ESolver_KS_LCAO Run +1442.6 4 +3.6e+02 +88 % + ESolver_KS_LCAO beforescf +3.1972 4 +0.8 +0.2 % + ESolver_KS_LCAO beforesolver +2.3896 4 +0.6 +0.15 % + ESolver_KS_LCAO set_matrix_grid +0.94857 4 +0.24 +0.058 % + Record_adj for_2d +0.68775 4 +0.17 +0.042 % + Grid_Driver Find_atom +2.9321 131712 +2.2e-05 +0.18 % + Charge atomic_rho +0.20093 7 +0.029 +0.012 % + PW_Basis recip2real +0.44584 178 +0.0025 +0.027 % + PW_Basis gathers_scatterp +0.20862 178 +0.0012 +0.013 % + Potential init_pot +0.28675 4 +0.072 +0.017 % + Potential update_from_charge +1.9802 31 +0.064 +0.12 % + Potential cal_v_eff +1.9654 31 +0.063 +0.12 % + H_Hartree_pw v_hartree +0.20862 31 +0.0067 +0.013 % + PW_Basis real2recip +0.6028 264 +0.0023 +0.037 % + PW_Basis gatherp_scatters +0.24779 264 +0.00094 +0.015 % + PotXC cal_v_eff +1.7414 31 +0.056 +0.11 % + XC_Functional v_xc +1.7311 31 +0.056 +0.11 % + HSolverLCAO solve +1435.7 27 +53 +88 % + HamiltLCAO updateHk +407.98 972 +0.42 +25 % + OperatorLCAO init +290.71 1944 +0.15 +18 % + Veff contributeHk +290.25 972 +0.3 +18 % + Gint_interface cal_gint +391.59 58 +6.8 +24 % + Gint_interface cal_gint_vlocal +156.08 27 +5.8 +9.5 % + Gint_Tools cal_psir_ylm +54.878 78732 +0.0007 +3.3 % + Gint_k folding_vl_k +134.16 972 +0.14 +8.2 % + Gint_k Distri +82.71 972 +0.085 +5 % + Overlap contributeHR +1.238 4 +0.31 +0.076 % + LCAO_gen_fixedH calculate_S_no +1.238 4 +0.31 +0.076 % + Ekin contributeHR +1.2586 4 +0.31 +0.077 % + Nonlocal contributeHR +12.419 4 +3.1 +0.76 % + LCAO_gen_fixedH b_NL_mu_new +38.163 8 +4.8 +2.3 % + ORB_gen_tables snap_psibeta_half +0.74517 409728 +1.8e-06 +0.045 % + OperatorLCAO folding_fixed +102.35 972 +0.11 +6.2 % + LCAO_nnr folding_fixedH +101.07 972 +0.1 +6.2 % + HSolverLCAO hamiltSolvePsiK +311.81 972 +0.32 +19 % + OperatorLCAO get_hs_pointers +275.45 558 +0.49 +17 % + DiagoElpa elpa_solve +309.03 972 +0.32 +19 % + ElecStateLCAO psiToRho +715.88 27 +27 +44 % + elecstate cal_dm +25.527 31 +0.82 +1.6 % + psiMulPsiMpi pdgemm +24.355 1116 +0.022 +1.5 % + Local_Orbital_wfc wfc_2d_to_grid +5.3729 1116 +0.0048 +0.33 % + LCAO_Charge cal_dk_k +537.89 27 +20 +33 % + Record_adj for_grid +0.11709 27 +0.0043 +0.0071 % + Gint_interface cal_gint_rho +152.95 27 +5.7 +9.3 % + Charge mix_rho +0.21758 23 +0.0095 +0.013 % + Charge Pulay_mixing +0.20631 23 +0.009 +0.013 % + Force_Stress_LCAO getForceStress +187.39 4 +47 +11 % + Forces cal_force_loc +0.31787 4 +0.079 +0.019 % + Forces cal_force_ew +0.30063 4 +0.075 +0.018 % + Forces cal_force_scc +0.38549 4 +0.096 +0.024 % + Stress_Func stress_loc +0.23667 4 +0.059 +0.014 % + Stress_Func stress_ewa +0.23226 4 +0.058 +0.014 % + Stress_Func stress_gga +0.1371 4 +0.034 +0.0084 % + Force_LCAO_k ftable_k +185.73 4 +46 +11 % + Force_LCAO_k allocate_k +34.742 4 +8.7 +2.1 % + Force_LCAO_k cal_foverlap_k +7.164 4 +1.8 +0.44 % + Force_LCAO_k cal_edm_2d +6.9794 4 +1.7 +0.43 % + Local_Orbital_Chargecal_dm_R +3.5519 8 +0.44 +0.22 % + Force_LCAO_k cal_ftvnl_dphi_k +0.11004 4 +0.028 +0.0067 % + Force_LCAO_k cal_fvl_dphi_k +82.566 4 +21 +5 % + Gint_interface cal_gint_force +82.566 4 +21 +5 % + Gint_Tools cal_dpsir_ylm +23.335 5832 +0.004 +1.4 % + Gint_Tools cal_dpsirr_ylm +11.778 5832 +0.002 +0.72 % + Force_LCAO_k cal_fvnl_dbeta_k_new+55.23 4 +14 +3.4 % ---------------------------------------------------------------------------------------- - CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- - +1374.8320 - ORB_table_phi Jl(x) +97.8037 - Charge_Pulay Rrho +32.0000 - Charge_Pulay dRrho +28.0000 - Charge_Pulay drho +28.0000 - Use_FFT porter +8.0000 - PW_Basis struc_fac +7.9969 - Grid_Meshcell index2normal +4.1684 - Grid_Meshcell index2ucell +4.1684 - Charge rho +4.0000 - Charge rho_save +4.0000 - Charge rho_core +4.0000 - Potential vltot +4.0000 - Potential vr +4.0000 - Potential vr_eff +4.0000 - Potential vr_eff1 +4.0000 - Potential vnew +4.0000 - Charge_Pulay rho_save2 +4.0000 - ORB_table_phi Table_SR&TR +3.2158 - Charge rhog +1.9992 - Charge rhog_save +1.9992 - Charge kin_r +1.9992 - Charge kin_r_save +1.9992 - Charge rhog_core +1.9992 - ORB_table_beta Table_NR +1.0437 + NAME---------------|MEMORY(MB)-------- +total +9277 +ORB::Jl(x) +2212 +pvpR_reduced +1350 +LOC::DM_R +1350 +Stress::dSR +1017 +ORB::Table_SR&TR +846.1 +Force::dS_K +508.3 +Stress::dHr +508.3 +Force::dTVNL +508.3 +ORB::Table_NR +175.9 +Force::edm2d +169.4 +Force::dm2d_K +169.4 +ChgMix::Rrho +79.19 +ChgMix::dRrho +69.06 +ChgMix::drho +67.28 +LOWF::wfc_k_grid +48.85 +FFT::grid +40.35 +SF::strucFac +18.86 +GT::index2normal +11.91 +GT::index2ucell +11.91 +Chg::rho +11 +Chg::rho_save +9.968 +Chg::rho_core +9.845 +Pot::veff_fix +9.611 +Pot::veff +9.611 +ChgMix::rho_save2 +9.611 +SF::eigts123 +8.741 +Grid::AtomLink +6.48 +meshball_pos +6.211 +GT::which_atom +4.981 +GT::which_bigcell +4.981 +GT::which_unitcell +4.981 +Chg::rhog +4.157 +Chg::rhog_save +4.036 +Chg::rhog_core +4.036 +SLTK::Epd_Atom +2.808 +SLTK::Epd_atom_info +2.441 + ------------- < 1.0 MB has been ignored ---------------- ---------------------------------------------------------- - Start Time : Wed Apr 13 14:58:14 2022 - Finish Time : Wed Apr 13 15:00:27 2022 - Total Time : 0 h 2 mins 13 secs + Start Time : Thu Apr 27 10:51:21 2023 + Finish Time : Thu Apr 27 11:18:40 2023 + Total Time : 0 h 27 mins 19 secs From 5f9c6cf3e25136df5bd805ee7d62ab334d938866 Mon Sep 17 00:00:00 2001 From: lauthirteen <844125986@qq.com> Date: Thu, 27 Apr 2023 19:21:21 +0800 Subject: [PATCH 3/3] reading the MD_dump file of ABACUS3.2, add new MD_dump file --- dpdata/abacus/md.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py index a8a798022..04b2f6ab1 100644 --- a/dpdata/abacus/md.py +++ b/dpdata/abacus/md.py @@ -133,8 +133,6 @@ def get_coords_from_dump(dumplines, natoms): "iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump." % (iframe, nframes_dump) ) - #cells *= bohr2ang - #coords *= bohr2ang stresses *= kbar2evperang3 return coords, cells, forces, stresses