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Isokinetic and Stochastic Isokinetic Dynamics #6

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52 changes: 26 additions & 26 deletions source/analysis.f
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Original file line number Diff line number Diff line change
Expand Up @@ -70,32 +70,32 @@ subroutine analysis (energy)
c
if (first) then
first = .false.
if (.not. allocated(aesum)) allocate (aesum(n))
if (.not. allocated(aeb)) allocate (aeb(n))
if (.not. allocated(aea)) allocate (aea(n))
if (.not. allocated(aeba)) allocate (aeba(n))
if (.not. allocated(aeub)) allocate (aeub(n))
if (.not. allocated(aeaa)) allocate (aeaa(n))
if (.not. allocated(aeopb)) allocate (aeopb(n))
if (.not. allocated(aeopd)) allocate (aeopd(n))
if (.not. allocated(aeid)) allocate (aeid(n))
if (.not. allocated(aeit)) allocate (aeit(n))
if (.not. allocated(aet)) allocate (aet(n))
if (.not. allocated(aept)) allocate (aept(n))
if (.not. allocated(aebt)) allocate (aebt(n))
if (.not. allocated(aeat)) allocate (aeat(n))
if (.not. allocated(aett)) allocate (aett(n))
if (.not. allocated(aev)) allocate (aev(n))
if (.not. allocated(aec)) allocate (aec(n))
if (.not. allocated(aecd)) allocate (aecd(n))
if (.not. allocated(aed)) allocate (aed(n))
if (.not. allocated(aem)) allocate (aem(n))
if (.not. allocated(aep)) allocate (aep(n))
if (.not. allocated(aer)) allocate (aer(n))
if (.not. allocated(aes)) allocate (aes(n))
if (.not. allocated(aelf)) allocate (aelf(n))
if (.not. allocated(aeg)) allocate (aeg(n))
if (.not. allocated(aex)) allocate (aex(n))
if (.not. allocated(aesum)) allocate (aesum(maxatm))
if (.not. allocated(aeb)) allocate (aeb(maxatm))
if (.not. allocated(aea)) allocate (aea(maxatm))
if (.not. allocated(aeba)) allocate (aeba(maxatm))
if (.not. allocated(aeub)) allocate (aeub(maxatm))
if (.not. allocated(aeaa)) allocate (aeaa(maxatm))
if (.not. allocated(aeopb)) allocate (aeopb(maxatm))
if (.not. allocated(aeopd)) allocate (aeopd(maxatm))
if (.not. allocated(aeid)) allocate (aeid(maxatm))
if (.not. allocated(aeit)) allocate (aeit(maxatm))
if (.not. allocated(aet)) allocate (aet(maxatm))
if (.not. allocated(aept)) allocate (aept(maxatm))
if (.not. allocated(aebt)) allocate (aebt(maxatm))
if (.not. allocated(aeat)) allocate (aeat(maxatm))
if (.not. allocated(aett)) allocate (aett(maxatm))
if (.not. allocated(aev)) allocate (aev(maxatm))
if (.not. allocated(aec)) allocate (aec(maxatm))
if (.not. allocated(aecd)) allocate (aecd(maxatm))
if (.not. allocated(aed)) allocate (aed(maxatm))
if (.not. allocated(aem)) allocate (aem(maxatm))
if (.not. allocated(aep)) allocate (aep(maxatm))
if (.not. allocated(aer)) allocate (aer(maxatm))
if (.not. allocated(aes)) allocate (aes(maxatm))
if (.not. allocated(aelf)) allocate (aelf(maxatm))
if (.not. allocated(aeg)) allocate (aeg(maxatm))
if (.not. allocated(aex)) allocate (aex(maxatm))
end if
c
c zero out energy partitioning components for each atom
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1 change: 1 addition & 0 deletions source/angang.f
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
c
c
module angang
use sizes
implicit none
integer nangang
integer, allocatable :: iaa(:,:)
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1 change: 1 addition & 0 deletions source/angbnd.f
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
c
c
module angbnd
use sizes
implicit none
integer nangle
integer, allocatable :: iang(:,:)
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4 changes: 1 addition & 3 deletions source/angles.f
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Expand Up @@ -27,15 +27,13 @@ subroutine angles
use iounit
implicit none
integer i,j,k,m
integer maxang
c
c
c perform dynamic allocation of some global arrays
c
maxang = 6 * n
if (.not. allocated(iang)) allocate (iang(4,maxang))
if (.not. allocated(anglist))
& allocate (anglist(maxval*(maxval-1)/2,n))
& allocate (anglist(maxval*(maxval-1)/2,maxatm))
c
c loop over all atoms, storing the atoms in each bond angle
c
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12 changes: 6 additions & 6 deletions source/attach.f
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Expand Up @@ -35,12 +35,12 @@ subroutine attach
maxn13 = 3 * maxval
maxn14 = 9 * maxval
maxn15 = 27 * maxval
if (.not. allocated(n13)) allocate (n13(n))
if (.not. allocated(n14)) allocate (n14(n))
if (.not. allocated(n15)) allocate (n15(n))
if (.not. allocated(i13)) allocate (i13(maxn13,n))
if (.not. allocated(i14)) allocate (i14(maxn14,n))
if (.not. allocated(i15)) allocate (i15(maxn15,n))
if (.not. allocated(n13)) allocate (n13(maxatm))
if (.not. allocated(n14)) allocate (n14(maxatm))
if (.not. allocated(n15)) allocate (n15(maxatm))
if (.not. allocated(i13)) allocate (i13(maxn13,maxatm))
if (.not. allocated(i14)) allocate (i14(maxn14,maxatm))
if (.not. allocated(i15)) allocate (i15(maxn15,maxatm))
c
c loop over all atoms finding all the 1-3 relationships;
c note "n12" and "i12" have already been setup elsewhere
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4 changes: 2 additions & 2 deletions source/bar.f
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Expand Up @@ -16,8 +16,8 @@
c via the Zwanzig free energy perturbation (FEP) and Bennett
c acceptance ratio (BAR) methods
c
c note current version takes as input a trajectory archive and
c key file for state A, and similar for state B; then finds the
c current version takes as input the trajectory archives and key
c files for state A, and similar for state B; then computes the
c total potential energy for all frames of each trajectory under
c control of both key files; finally the FEP and BAR algorithms
c are used to compute the free energy for state A --> state B
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13 changes: 13 additions & 0 deletions source/bath.f
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Expand Up @@ -35,18 +35,31 @@
c thermostat choice of temperature control method to be used
c barostat choice of pressure control method to be used
c volscale choice of scaling method for Monte Carlo barostat
c q_iso1/2 masses of isokinetic thermostats
c v_iso1/2 velocities of isokinetic thermostats
c f_iso1/2 forces acting on isokinetic thermostats
c len_nhc In isokinetic dynamics, this is the Nose-Hoover chain length M.
c In stochastic isokinetic dynamics, this is the chain length L
c
c
module bath
implicit none
integer maxnose
parameter (maxnose=4)
integer len_nhc,isok_L,isok_M
integer isok_chain
parameter (isok_chain=4)
integer voltrial
real*8 kelvin,atmsph
real*8 tautemp,taupres
real*8 compress,collide
real*8 eta,volmove
real*8 vbar,qbar,gbar
real*8 q_iso1(isok_chain,3,10000)
real*8 q_iso2(isok_chain,3,10000)
real*8 v_iso1(isok_chain,3,10000)
real*8 v_iso2(isok_chain,3,10000)
real*8 f_iso1(isok_chain,3,10000)
real*8 vnh(maxnose)
real*8 qnh(maxnose)
real*8 gnh(maxnose)
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3 changes: 0 additions & 3 deletions source/bitors.f
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Expand Up @@ -20,19 +20,16 @@
subroutine bitors
use sizes
use angbnd
use atoms
use bitor
use couple
use iounit
implicit none
integer i,j,k
integer ia,ib,ic,id,ie
integer maxbitor
c
c
c perform dynamic allocation of some global arrays
c
maxbitor = 8 * n
if (.not. allocated(ibitor)) allocate (ibitor(5,maxbitor))
c
c loop over all angles, storing the atoms in each bitorsion
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4 changes: 1 addition & 3 deletions source/bonds.f
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Expand Up @@ -25,14 +25,12 @@ subroutine bonds
use iounit
implicit none
integer i,j,k,m
integer maxbnd
c
c
c perform dynamic allocation of some global arrays
c
maxbnd = 4 * n
if (.not. allocated(ibnd)) allocate (ibnd(2,maxbnd))
if (.not. allocated(bndlist)) allocate (bndlist(maxval,n))
if (.not. allocated(bndlist)) allocate (bndlist(maxval,maxatm))
c
c loop over all atoms, storing the atoms in each bond
c
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2 changes: 1 addition & 1 deletion source/cluster.f
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Expand Up @@ -238,7 +238,7 @@ subroutine cluster
c output the final list of atoms in each group
c
if (debug .and. use_group) then
do i = 1, ngrp
do i = 0, ngrp
size = igrp(2,i) - igrp(1,i) + 1
if (size .ne. 0) then
write (iout,50) i
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