Skip to content

fix(abacus): do not collect the unconverged structure for AIMD #368

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
wanghan-iapcm merged 9 commits into from
Oct 29, 2022
Merged

fix(abacus): do not collect the unconverged structure for AIMD #368

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
9c95bd9
fix: fix the judgement of convergence in abacus/scf
pxlxingliang Sep 30, 2022
5af6746
fix INPUT.fail
pxlxingliang Sep 30, 2022
30fb361
Merge branch 'devel' of github.com:deepmodeling/dpdata into devel
pxlxingliang Oct 26, 2022
731d4cd
fix(abacus): do not collect the unconverged structure for AIMD
pxlxingliang Oct 26, 2022
eba37ef
fix: set the energy of unconveraged structure to be "None"
pxlxingliang Oct 27, 2022
13bed27
output the unconverged structure together
pxlxingliang Oct 27, 2022
5bfd1d1
fix
pxlxingliang Oct 27, 2022
127e7f2
use np.nan for the energy of uncoveraged structure and add UT
pxlxingliang Oct 28, 2022
1fe2955
add the log file
pxlxingliang Oct 28, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 19 additions & 0 deletions dpdata/abacus/md.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import numpy as np
from .scf import ry2ev, bohr2ang, kbar2evperang3, get_block, get_geometry_in, get_cell, get_coords
import re
import warnings

# Read in geometries from an ABACUS MD trajectory.
# The atomic coordinates are read in from generated files in OUT.XXXX.
Expand Down Expand Up @@ -80,6 +81,10 @@ def get_energy(outlines, ndump, dump_freq):
if nenergy%dump_freq == 0:
energy.append(float(line.split()[-2]))
nenergy+=1
elif "!! convergence has not been achieved" in line:
if nenergy%dump_freq == 0:
energy.append(np.nan)
nenergy+=1
assert(ndump == len(energy)), "Number of total energies in running_md.log = %d. Number of frames in MD_dump = %d. Please check."%(len(energy), ndump)
energy = np.array(energy)
return energy
Expand Down Expand Up @@ -113,6 +118,20 @@ def get_frame (fname):
with open(os.path.join(path_out, "running_md.log"), 'r') as fp:
outlines = fp.read().split('\n')
energy = get_energy(outlines, ndump, dump_freq)

unconv_stru = ''
for i,iene in enumerate(energy):
if np.isnan(iene):
coords = np.delete(coords,i-ndump,axis=0)
cells = np.delete(cells,i-ndump,axis=0)
force = np.delete(force,i-ndump,axis=0)
stress = np.delete(stress,i-ndump,axis=0)
energy = np.delete(energy,i-ndump,axis=0)
unconv_stru += "%d " % i
ndump = len(energy)
if unconv_stru != '':
warnings.warn(f"Structure %s are unconverged and not collected!" % unconv_stru)

for iframe in range(ndump):
stress[iframe] *= np.linalg.det(cells[iframe, :, :].reshape([3, 3]))
if np.sum(np.abs(stress[0])) < 1e-10:
Expand Down
30 changes: 30 additions & 0 deletions tests/abacus.md.unconv/INPUT
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
INPUT_PARAMETERS
calculation md
ntype 2
nbands 8

ecutwfc 50.000000
scf_thr 1.000000e-07
scf_nmax 100

basis_type lcao
dft_functional lda
gamma_only 1

mixing_type pulay
mixing_beta 0.400000
smearing_method gaussian
smearing_sigma 0.020000

cal_force 1
cal_stress 1

md_type 0
md_nstep 10
md_tfirst 10
md_dt 1
chg_extrap second-order

deepks_scf 1
deepks_bandgap 0
deepks_model model.ptg
176 changes: 176 additions & 0 deletions tests/abacus.md.unconv/OUT.ABACUS/MD_dump
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,176 @@
MDSTEP: 0
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
0.117880839971 0.348548064508 0.269730962791
0.348548064508 -1.559580670587 -1.949852828444
0.269730962791 -1.949852828444 -2.332929959367
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.872796345708 0.993283528438 3.293903479774 0.203673227663 -0.476188513340 -0.673198308232
1 H 10.341931867316 14.686041612304 2.160229648207 -0.497679578285 3.938931579746 4.649209009347
2 O 10.133374044868 0.350751910571 3.193008852361 0.294006350622 -3.462743066406 -3.976010701114


MDSTEP: 1
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
-0.052861928550 0.190313757600 0.235641072577
0.190313757600 -1.590040770984 -1.856968175095
0.235641072577 -1.856968175095 -2.206369542675
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.875596899173 0.988023063544 3.294283265923 -0.254022717293 -0.877700208440 -0.747314202230
1 H 10.340932440770 14.707241014770 2.180444767744 -0.497860772145 3.864467170520 4.570589962154
2 O 10.131572917949 0.334812972999 3.172413946676 0.751883489438 -2.986766962080 -3.823275759924


MDSTEP: 2
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
-0.316210888687 -0.207283827612 0.007046496091
-0.207283827612 -1.346616360903 -1.287258423394
0.007046496091 -1.287258423394 -1.415183801991
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.875946508110 0.974294086278 3.287452572336 -1.045230179415 -1.628147086821 -0.958970724628
1 H 10.335129392135 14.765726825200 2.244759338627 -0.207420915322 2.933943064626 3.340010877721
2 O 10.137026357647 0.290056139835 3.114930069379 1.252651094738 -1.305795977804 -2.381040153093


MDSTEP: 3
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
-0.260134638405 -0.993002747244 -0.895525915647
-0.993002747244 0.262836092646 1.051311229863
-0.895525915647 1.051311229863 1.805220211014
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.866211187568 0.944855891202 3.271369225774 -1.519717284879 -2.134878371745 -1.173199796326
1 H 10.327325037621 14.852520858530 2.341300087841 2.109118093970 -3.394877057008 -5.282580352734
2 O 10.154566032703 0.232700301582 3.034472666728 -0.589400809091 5.529755428753 6.455780149060


MDSTEP: 4
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
0.504846487933 -0.963922770050 -1.396738517223
-0.963922770050 2.096159352353 2.997442421390
-1.396738517223 2.997442421390 4.270661113979
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.841812836866 0.894819268862 3.243966231690 -0.065851648219 -0.473828154419 -0.442665692581
1 H 10.339870561687 14.906559335828 2.386871728651 4.482678409108 -9.390324011782 -13.734305291761
2 O 10.166418859339 0.228698446623 3.016304020001 -4.416826760889 9.864152166202 14.176970984342


MDSTEP: 5
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
2.301988732603 2.106077476560 0.632201255105
2.106077476560 1.094304604347 -0.313178332666
0.632201255105 -0.313178332666 -0.819241722779
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.816779114892 0.840210903747 3.212292166621 6.855059278224 5.454541643043 1.016758449181
1 H 10.395667320285 14.869995037486 2.299927582003 -0.960810002863 1.486842944666 2.333454697801
2 O 10.135655822714 0.319871110080 3.134922231718 -5.894249275361 -6.941384587709 -3.350213146982


MDSTEP: 6
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
0.224387150431 1.128837044998 1.081862730682
1.128837044998 -0.268818497136 -1.093793836625
1.081862730682 -1.093793836625 -2.004917355086
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.857886603488 0.838230819836 3.190428320831 1.363129257990 1.501361774798 0.692219305499
1 H 10.442193679586 14.847776580413 2.235497831256 -2.370639635238 2.295060837375 4.247420933792
2 O 10.048021974818 0.344069651064 3.221215828255 1.007510377248 -3.796422612173 -4.939640239291


MDSTEP: 7
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
-1.914534915401 0.160753699840 1.525216417878
0.160753699840 -0.780431878582 -0.977244043867
1.525216417878 -0.977244043867 -2.191357680684
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.912146278758 0.850736662489 3.175243370290 -2.896292249377 -0.849289935513 1.095057694700
1 H 10.465846863187 14.847702075120 2.212049427419 -2.832220895025 2.019939251673 4.270685618311
2 O 9.970109115947 0.331638313704 3.259849182634 5.728513144402 -1.170649316160 -5.365743313011


MDSTEP: 8
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
-2.513125907165 -0.154419226124 1.580371274213
-0.154419226124 -0.825335562412 -0.815094290966
1.580371274213 -0.815094290966 -2.050106792249
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.938461005959 0.855048109998 3.170624111252 -3.822684404614 -1.352624889240 1.151176221490
1 H 10.462173292782 14.867117004122 2.229806840379 -2.984053847480 1.788365306177 4.125001485576
2 O 9.947467959151 0.307911937194 3.246711028711 6.806738252094 -0.435740416937 -5.276177707066


MDSTEP: 9
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
-1.921730659733 -0.250128628384 1.045305625840
-0.250128628384 -0.550642430618 -0.443385704265
1.045305625840 -0.443385704265 -1.253788166285
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.927892467255 0.846308722497 3.177112004724 -3.263179899026 -1.178327094849 0.932844111407
1 H 10.429708004337 14.903787020423 2.287364433146 -2.485295875334 1.119241763062 3.025686004957
2 O 9.990501786298 0.279981308393 3.182665542472 5.748475774360 0.059085331787 -3.958530116363


MDSTEP: 10
LATTICE_CONSTANT: 1.889726125458
LATTICE_VECTORS
14.524509151052 0.000000000000 0.000000000000
-0.014055052628 15.127720223676 0.000000000000
-0.442369434823 0.417648184158 14.953520775918
VIRIAL (KBAR)
0.125490523345 -0.470583331016 -0.646063109567
-0.470583331016 0.977542641385 1.479381534553
-0.646063109567 1.479381534553 2.154282026823
INDEX LABEL POSITIONS FORCE (eV/Angstrom)
0 H 10.885839055837 0.826200216607 3.192600467891 -0.652935734428 0.144670019023 0.624517068595
1 H 10.373263276599 14.951256068815 2.374115432862 1.613773327904 -3.964330561830 -5.728774672298
2 O 10.088999925455 0.252620765891 3.080426079588 -0.960837593476 3.819660542807 5.104257603703


Loading