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Fixed the homology gradient in finegrain mode
author
Adam Liwo
<adam@piasek4.chem.univ.gda.pl>
Fri, 12 Jun 2015 14:23:42 +0000
(16:23 +0200)
committer
Adam Liwo
<adam@piasek4.chem.univ.gda.pl>
Fri, 12 Jun 2015 14:23:42 +0000
(16:23 +0200)
source/unres/src_MD/Makefile_MPICH_ifort
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source/unres/src_MD/energy_p_new_barrier.F
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source/unres/src_MD/gradient_p.F
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source/wham/src/enecalc1.F
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diff --git
a/source/unres/src_MD/Makefile_MPICH_ifort
b/source/unres/src_MD/Makefile_MPICH_ifort
index
a747321
..
d6ae5dd
100644
(file)
--- a/
source/unres/src_MD/Makefile_MPICH_ifort
+++ b/
source/unres/src_MD/Makefile_MPICH_ifort
@@
-1,6
+1,6
@@
###################################################################
###################################################################
-#INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
-INSTALL_DIR = /users/software/mpich2-1.4.1p1_intel
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+#INSTALL_DIR = /users/software/mpich2-1.4.1p1_intel
FC= ifort
FC= ifort
@@
-15,8
+15,8
@@
FFLAGSE = -c -O3 -ipo -opt_report -I$(INSTALL_DIR)/include
#FFLAGSE = ${FFLAGS1}
# -lmpl necessary in mpich
#FFLAGSE = ${FFLAGS1}
# -lmpl necessary in mpich
-LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -lmpl -CB
-#LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -CB
+#LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -lmpl -CB
+LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -CB
ARCH = LINUX
PP = /lib/cpp -P
ARCH = LINUX
PP = /lib/cpp -P
@@
-68,8
+68,8
@@
GAB: ${object} xdrf/libxdrf.a
E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-DSPLITELE -DLANG0
E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \
-DSPLITELE -DLANG0
-E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH2_E0LL2Y.exe
-#E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
+#E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH2_E0LL2Y.exe
+E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
E0LL2Y: ${object} xdrf/libxdrf.a
cc -o compinfo compinfo.c
./compinfo | true
E0LL2Y: ${object} xdrf/libxdrf.a
cc -o compinfo compinfo.c
./compinfo | true
diff --git
a/source/unres/src_MD/energy_p_new_barrier.F
b/source/unres/src_MD/energy_p_new_barrier.F
index
60cb90b
..
002f211
100644
(file)
--- a/
source/unres/src_MD/energy_p_new_barrier.F
+++ b/
source/unres/src_MD/energy_p_new_barrier.F
@@
-543,6
+543,7
@@
cMS$ATTRIBUTES C :: proc_proc
include 'COMMON.TIME1'
include 'COMMON.MAXGRAD'
include 'COMMON.SCCOR'
include 'COMMON.TIME1'
include 'COMMON.MAXGRAD'
include 'COMMON.SCCOR'
+ include 'COMMON.MD'
#ifdef TIMING
#ifdef MPI
time01=MPI_Wtime()
#ifdef TIMING
#ifdef MPI
time01=MPI_Wtime()
@@
-813,6
+814,14
@@
c enddo
#endif
enddo
enddo
#endif
enddo
enddo
+ if (constr_homology.gt.0) then
+ do i=1,nct
+ do j=1,3
+ gradc(j,i,icg)=gradc(j,i,icg)+duscdiff(j,i)
+ gradx(j,i,icg)=gradx(j,i,icg)+duscdiffx(j,i)
+ enddo
+ enddo
+ endif
#ifdef DEBUG
write (iout,*) "gloc before adding corr"
do i=1,4*nres
#ifdef DEBUG
write (iout,*) "gloc before adding corr"
do i=1,4*nres
@@
-6330,8
+6339,11
@@
c grad_theta3=sum_sgtheta/sum_gtheta 1/*theta(i)? s. line below
c grad_theta3=sum_sgtheta/sum_gtheta
c
c Final value of gradient using same var as in Econstr_back
c grad_theta3=sum_sgtheta/sum_gtheta
c
c Final value of gradient using same var as in Econstr_back
- dutheta(i-2)=sum_sgtheta/sum_gtheta*waga_theta
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)
+ & +sum_sgtheta/sum_gtheta*waga_theta
& *waga_homology(iset)
& *waga_homology(iset)
+c dutheta(i-2)=sum_sgtheta/sum_gtheta*waga_theta
+c & *waga_homology(iset)
c dutheta(i)=sum_sgtheta/sum_gtheta
c
c Uconst_back=Uconst_back+waga_theta*utheta(i) ! waga_theta added as weight
c dutheta(i)=sum_sgtheta/sum_gtheta
c
c Uconst_back=Uconst_back+waga_theta*utheta(i) ! waga_theta added as weight
diff --git
a/source/unres/src_MD/gradient_p.F
b/source/unres/src_MD/gradient_p.F
index
8606ba4
..
dd59b31
100644
(file)
--- a/
source/unres/src_MD/gradient_p.F
+++ b/
source/unres/src_MD/gradient_p.F
@@
-318,15
+318,15
@@
c If performing constraint dynamics, add the gradients of the constraint energy
write (iout,*) i,(duscdiffx(j,i),j=1,3)
enddo
#endif
write (iout,*) i,(duscdiffx(j,i),j=1,3)
enddo
#endif
-c if(usampl.and.totT.gt.eq_time) then
- if(usampl.and.totT.gt.eq_time .or. constr_homology.gt.0) then
+ if(usampl.and.totT.gt.eq_time) then
+c if(usampl.and.totT.gt.eq_time .or. constr_homology.gt.0) then
c
c Setting suited bounds for HM restrs
c
do i=1,nct
do j=1,3
c
c Setting suited bounds for HM restrs
c
do i=1,nct
do j=1,3
- gradc(j,i,icg)=gradc(j,i,icg)+dudconst(j,i)+duscdiff(j,i)
- gradx(j,i,icg)=gradx(j,i,icg)+dudxconst(j,i)+duscdiffx(j,i)
+ gradc(j,i,icg)=gradc(j,i,icg)+dudconst(j,i)
+ gradx(j,i,icg)=gradx(j,i,icg)+dudxconst(j,i)
enddo
#ifdef DEBUG
write (iout,*) "i",i," gradc",(gradc(j,i,icg),j=1,3)
enddo
#ifdef DEBUG
write (iout,*) "i",i," gradc",(gradc(j,i,icg),j=1,3)
diff --git
a/source/wham/src/enecalc1.F
b/source/wham/src/enecalc1.F
index
c8901ad
..
0f7d34c
100644
(file)
--- a/
source/wham/src/enecalc1.F
+++ b/
source/wham/src/enecalc1.F
@@
-519,7
+519,7
@@
c else
c & potE(i,iparm),-entfac(i),rms_nat,iscore
& potE(i,nparmset),-entfac(i),rms_nat,iscore
c endif
c & potE(i,iparm),-entfac(i),rms_nat,iscore
& potE(i,nparmset),-entfac(i),rms_nat,iscore
c endif
- write (iout,'(2i5,3e15.5)') i,me,potE(i,iparm),-entfac(i)
+c write (iout,'(2i5,3e15.5)') i,me,potE(i,iparm),-entfac(i)
#ifndef MPI
if (cxfile) call cxwrite(ixdrf,csingle,potE(i,nparmset),
& -entfac(i),rms_nat,iscore)
#ifndef MPI
if (cxfile) call cxwrite(ixdrf,csingle,potE(i,nparmset),
& -entfac(i),rms_nat,iscore)