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critical bug fix for ions langvin and fix pdb output for wham and cluster
author
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Wed, 31 Mar 2021 06:40:41 +0000
(08:40 +0200)
committer
Adam Sieradzan
<adasko@piasek4.chem.univ.gda.pl>
Wed, 31 Mar 2021 06:40:41 +0000
(08:40 +0200)
source/cluster/io_clust.F90
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source/unres/MD.F90
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source/unres/MREMD.F90
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source/unres/REMD.F90
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source/unres/energy.F90
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source/unres/geometry.F90
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source/unres/io_config.F90
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source/wham/io_wham.F90
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diff --git
a/source/cluster/io_clust.F90
b/source/cluster/io_clust.F90
index
ed4ccc3
..
3b3a134
100644
(file)
--- a/
source/cluster/io_clust.F90
+++ b/
source/cluster/io_clust.F90
@@
-1493,6
+1493,7
@@
call reada(weightcard,'WPEPBASE',wpepbase,1.0d0)
call reada(weightcard,'WSCPHO',wscpho,0.0d0)
call reada(weightcard,'WPEPPHO',wpeppho,0.0d0)
call reada(weightcard,'WPEPBASE',wpepbase,1.0d0)
call reada(weightcard,'WSCPHO',wscpho,0.0d0)
call reada(weightcard,'WPEPPHO',wpeppho,0.0d0)
+ call reada(weightcard,'WCATNUCL',wcatnucl,0.0d0)
call reada(weightcard,"D0CM",d0cm,3.78d0)
call reada(weightcard,"AKCM",akcm,15.1d0)
call reada(weightcard,"D0CM",d0cm,3.78d0)
call reada(weightcard,"AKCM",akcm,15.1d0)
@@
-1562,6
+1563,8
@@
weights(46)=wscbase
weights(47)=wscpho
weights(48)=wpeppho
weights(46)=wscbase
weights(47)=wscpho
weights(48)=wpeppho
+ weights(49)=wpeppho
+ weights(50)=wcatnucl
write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,&
@@
-1870,6
+1873,8
@@
write(iout,*)"po setup var"
open (itube,file=tubename,status='old')
call getenv('IONPAR',ionname)
open (iion,file=ionname,status='old')
open (itube,file=tubename,status='old')
call getenv('IONPAR',ionname)
open (iion,file=ionname,status='old')
+ call getenv('IONPAR_NUCL',ionnuclname)
+ open (iionnucl,file=ionnuclname,status='old')
#ifndef OLDSCP
!
#ifndef OLDSCP
!
@@
-1946,7
+1951,7
@@
write(iout,*)"po setup var"
write (ipdb,'(a)') 'TER'
else
ires=ires+1
write (ipdb,'(a)') 'TER'
else
ires=ires+1
- if (ires.eq.2) then
+ if ((ires.eq.2).and.(mnum.ne.5)) then
do j=1,3
cbeg(j)=c(j,i-1)
enddo
do j=1,3
cbeg(j)=c(j,i-1)
enddo
diff --git
a/source/unres/MD.F90
b/source/unres/MD.F90
index
2b412fd
..
3bb57e0
100644
(file)
--- a/
source/unres/MD.F90
+++ b/
source/unres/MD.F90
@@
-2058,6
+2058,7
@@
do j=1,3
adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
adt2=0.5d0*adt+sqrt13*d_as_work(ind+j)*d_time
do j=1,3
adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
adt2=0.5d0*adt+sqrt13*d_as_work(ind+j)*d_time
+! write(iout,*) "adt",adt,"ads",adt2
dc(j,inres)=dc_old(j,inres)+(d_t_old(j,inres)+adt2)*d_time
d_t_new(j,inres)=d_t_old(j,inres)+0.5d0*adt
d_t(j,inres)=d_t_old(j,inres)+adt
dc(j,inres)=dc_old(j,inres)+(d_t_old(j,inres)+adt2)*d_time
d_t_new(j,inres)=d_t_old(j,inres)+0.5d0*adt
d_t(j,inres)=d_t_old(j,inres)+adt
@@
-5033,11
+5034,14
@@
!el ginvfric(2*nres,2*nres) !maxres2=2*maxres
!el common /przechowalnia/ ginvfric
!el ginvfric(2*nres,2*nres) !maxres2=2*maxres
!el common /przechowalnia/ ginvfric
- logical :: lprn = .false., checkmode = .false.
+ logical :: lprn, checkmode
integer :: i,j,ind,k,nres2,nres6,mnum
nres2=2*nres
nres6=6*nres
integer :: i,j,ind,k,nres2,nres6,mnum
nres2=2*nres
nres6=6*nres
-
+ lprn=.false.
+ checkmode=.false.
+! if (large) lprn=.true.
+! if (large) checkmode=.true.
if(.not.allocated(gamvec)) allocate(gamvec(nres6)) !(MAXRES6)
if(.not.allocated(ginvfric)) allocate(ginvfric(nres2,nres2)) !maxres2=2*maxres
do i=0,nres2
if(.not.allocated(gamvec)) allocate(gamvec(nres6)) !(MAXRES6)
if(.not.allocated(ginvfric)) allocate(ginvfric(nres2,nres2)) !maxres2=2*maxres
do i=0,nres2
diff --git
a/source/unres/MREMD.F90
b/source/unres/MREMD.F90
index
8c4a4b5
..
003d67b
100644
(file)
--- a/
source/unres/MREMD.F90
+++ b/
source/unres/MREMD.F90
@@
-411,11
+411,13
@@
do i=nnt,nct-1
mnum=(molnum(i))
stdforcp(i)=stdfp(mnum)*dsqrt(gamp(mnum))
do i=nnt,nct-1
mnum=(molnum(i))
stdforcp(i)=stdfp(mnum)*dsqrt(gamp(mnum))
+! write(iout,*) "stdforcp=",stdforcp(i),itype(i,mnum),i
enddo
do i=nnt,nct
mnum=molnum(i)
if (itype(i,mnum).ne.ntyp1) stdforcsc(i)=stdfsc(iabs(itype(i,mnum)),mnum)&
*dsqrt(gamsc(iabs(itype(i,mnum)),mnum))
enddo
do i=nnt,nct
mnum=molnum(i)
if (itype(i,mnum).ne.ntyp1) stdforcsc(i)=stdfsc(iabs(itype(i,mnum)),mnum)&
*dsqrt(gamsc(iabs(itype(i,mnum)),mnum))
+! write(iout,*) "stdforcsc=",stdforcsc(i),itype(i,mnum),i
enddo
endif
call rescale_weights(t_bath)
enddo
endif
call rescale_weights(t_bath)
diff --git
a/source/unres/REMD.F90
b/source/unres/REMD.F90
index
fc0c9f1
..
699631c
100644
(file)
--- a/
source/unres/REMD.F90
+++ b/
source/unres/REMD.F90
@@
-627,11
+627,11
@@
ii = ind+m
mnum=molnum(i)
iti=itype(i,mnum)
ii = ind+m
mnum=molnum(i)
iti=itype(i,mnum)
- if (mnum.eq.5) then
- mscab=0.0
- else
+! if (mnum.eq.5) then
+! mscab=0.0
+! else
mscab=msc(iabs(iti),mnum)
mscab=msc(iabs(iti),mnum)
- endif
+! endif
massvec(ii)=mscab
if (iti.ne.10 .and. iti.ne.ntyp1_molec(mnum) .and. mnum.ne.5) then
massvec(ii)=mscab
if (iti.ne.10 .and. iti.ne.ntyp1_molec(mnum) .and. mnum.ne.5) then
diff --git
a/source/unres/energy.F90
b/source/unres/energy.F90
index
d235e01
..
ec3ffd4
100644
(file)
--- a/
source/unres/energy.F90
+++ b/
source/unres/energy.F90
@@
-11663,7
+11663,7
@@
endif
endif
endif
endif
endif
endif
-#define DEBUG
+!#define DEBUG
#ifdef DEBUG
write (iout,*) "gradc gradx gloc"
do i=1,nres
#ifdef DEBUG
write (iout,*) "gradc gradx gloc"
do i=1,nres
@@
-11671,7
+11671,7
@@
i,(gradc(j,i,icg),j=1,3),(gradx(j,i,icg),j=1,3),gloc(i,icg)
enddo
#endif
i,(gradc(j,i,icg),j=1,3),(gradx(j,i,icg),j=1,3),gloc(i,icg)
enddo
#endif
-#undef DEBUG
+!#undef DEBUG
#ifdef TIMING
time_sumgradient=time_sumgradient+MPI_Wtime()-time01
#endif
#ifdef TIMING
time_sumgradient=time_sumgradient+MPI_Wtime()-time01
#endif
@@
-16730,13
+16730,13
@@
chip1=chip(itypi)
#endif
!#define DEBUG
!el write (iout,*) "After sum_gradient"
#endif
!#define DEBUG
!el write (iout,*) "After sum_gradient"
-!#ifdef DEBUG
+#ifdef DEBUG
write (iout,*) "After sum_gradient"
do i=1,nres-1
write (iout,*) i," gradc ",(gradc(j,i,icg),j=1,3)
write (iout,*) i," gradx ",(gradx(j,i,icg),j=1,3)
enddo
write (iout,*) "After sum_gradient"
do i=1,nres-1
write (iout,*) i," gradc ",(gradc(j,i,icg),j=1,3)
write (iout,*) i," gradx ",(gradx(j,i,icg),j=1,3)
enddo
-!#endif
+#endif
!#undef DEBUG
! If performing constraint dynamics, add the gradients of the constraint energy
if(usampl.and.totT.gt.eq_time) then
!#undef DEBUG
! If performing constraint dynamics, add the gradients of the constraint energy
if(usampl.and.totT.gt.eq_time) then
diff --git
a/source/unres/geometry.F90
b/source/unres/geometry.F90
index
c89442f
..
fe8e89a
100644
(file)
--- a/
source/unres/geometry.F90
+++ b/
source/unres/geometry.F90
@@
-3398,7
+3398,7
@@
enddo
endif
! Settind dE/ddnres-1
enddo
endif
! Settind dE/ddnres-1
-#define DEBUG
+!#define DEBUG
#ifdef DEBUG
j=1
write(iout,*)"in int to carta",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
#ifdef DEBUG
j=1
write(iout,*)"in int to carta",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
@@
-3445,7
+3445,7
@@
write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
gloc(ialph(i,1)+nside,icg),domega(j,3,i)
#endif
write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
gloc(ialph(i,1)+nside,icg),domega(j,3,i)
#endif
-#undef DEBUG
+!#undef DEBUG
enddo
endif
enddo
enddo
endif
enddo
diff --git
a/source/unres/io_config.F90
b/source/unres/io_config.F90
index
73c18ab
..
0d92898
100644
(file)
--- a/
source/unres/io_config.F90
+++ b/
source/unres/io_config.F90
@@
-3293,6
+3293,8
@@
print *,msc(i,5),restok(i,5)
enddo
ip(5)=0.2
print *,msc(i,5),restok(i,5)
enddo
ip(5)=0.2
+ ! mp(5)=0.2
+ ! pstok(5)=1.0
!DIR$ NOUNROLL
do j=1,ntyp_molec(5)
do i=1,ntyp
!DIR$ NOUNROLL
do j=1,ntyp_molec(5)
do i=1,ntyp
@@
-3935,8
+3937,8
@@
! enddo
! else
do j=1,3
! enddo
! else
do j=1,3
- dcj=(c(j,nres-2)-c(j,nres-3))/2.0
- c(j,nres)=c(j,nres-1)+dcj
+ dcj=(c(j,nres-nres_molec(5)-2)-c(j,nres-nres_molec(5)-3))/2.0
+ c(j,nres)=c(j,nres-nres_molec(5)-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
! endif
c(j,2*nres)=c(j,nres)
enddo
! endif
diff --git
a/source/wham/io_wham.F90
b/source/wham/io_wham.F90
index
68457dd
..
fee1e46
100644
(file)
--- a/
source/wham/io_wham.F90
+++ b/
source/wham/io_wham.F90
@@
-3908,8
+3908,9
@@
allocate(ww(max_eneW))
!--------------------------------------------------------------------------------
subroutine pdboutW(ii,temp,efree,etot,entropy,rmsdev)
!--------------------------------------------------------------------------------
subroutine pdboutW(ii,temp,efree,etot,entropy,rmsdev)
- use geometry_data, only:nres,c
+ use geometry_data, only:nres,c,boxxsize,boxysize,boxzsize
use energy_data, only:nss,nnt,nct,ihpb,jhpb,itype,molnum
use energy_data, only:nss,nnt,nct,ihpb,jhpb,itype,molnum
+ use energy, only:boxshift
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'DIMENSIONS.ZSCOPT'
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
! include 'DIMENSIONS.ZSCOPT'
@@
-3924,7
+3925,7
@@
allocate(ww(max_eneW))
'D','E','F','G','H','I','J','K','L','M','N','O',&
'P','Q','R','S','V','W','X','Y','Z'/),shape(chainid))
integer,dimension(nres) :: ica !(maxres)
'D','E','F','G','H','I','J','K','L','M','N','O',&
'P','Q','R','S','V','W','X','Y','Z'/),shape(chainid))
integer,dimension(nres) :: ica !(maxres)
- real(kind=8) :: temp,efree,etot,entropy,rmsdev
+ real(kind=8) :: temp,efree,etot,entropy,rmsdev,xj,yj,zj
integer :: ii,i,j,iti,ires,iatom,ichain,mnum
write(ipdb,'("REMARK CONF",i8," TEMPERATURE",f7.1," RMS",0pf7.2)')&
ii,temp,rmsdev
integer :: ii,i,j,iti,ires,iatom,ichain,mnum
write(ipdb,'("REMARK CONF",i8," TEMPERATURE",f7.1," RMS",0pf7.2)')&
ii,temp,rmsdev
@@
-3948,9
+3949,17
@@
allocate(ww(max_eneW))
ires=ires+1
iatom=iatom+1
ica(i)=iatom
ires=ires+1
iatom=iatom+1
ica(i)=iatom
+ if (mnum.ne.5) then
write (ipdb,10) iatom,restyp(iti,mnum),chainid(ichain),&
ires,(c(j,i),j=1,3)
write (ipdb,10) iatom,restyp(iti,mnum),chainid(ichain),&
ires,(c(j,i),j=1,3)
- if (iti.ne.10) then
+ else
+ xj=boxshift(c(1,i)-c(1,2),boxxsize)
+ yj=boxshift(c(2,i)-c(2,2),boxysize)
+ zj=boxshift(c(3,i)-c(3,2),boxzsize)
+ write (ipdb,10) iatom,restyp(iti,mnum),chainid(ichain),&
+ ires,c(1,2)+xj,c(2,2)+yj,c(3,2)+zj
+ endif
+ if ((iti.ne.10).and.(mnum.ne.5)) then
iatom=iatom+1
write (ipdb,20) iatom,restyp(iti,mnum),chainid(ichain),&
ires,(c(j,nres+i),j=1,3)
iatom=iatom+1
write (ipdb,20) iatom,restyp(iti,mnum),chainid(ichain),&
ires,(c(j,nres+i),j=1,3)