Skip to content

Commit 86d813f

Browse files
chigchig
committed
Merge remote-tracking branch 'sugitalab/main'
2 parents 294502e + 132b508 commit 86d813f

File tree

41 files changed

+2568
-997
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

41 files changed

+2568
-997
lines changed

‎configure.ac‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -700,9 +700,11 @@ if test x"${with_cuda}" != x"no"; then
700700
if test ${NVCC_VER} -lt 080000; then
701701
AC_MSG_ERROR([CUDA version must be >= 8.0.0 for GENESIS])
702702
fi
703-
GENCODEFLAG='--generate-code=arch=compute_35,code=\"sm_35,compute_35\"'
704-
if test ${NVCC_VER} -gt 065000; then
705-
GENCODEFLAG+=' --generate-code=arch=compute_37,code=\"sm_37,compute_37\"' #K80
703+
if test ${NVCC_VER} -lt 120000; then
704+
GENCODEFLAG='--generate-code=arch=compute_35,code=\"sm_35,compute_35\"'
705+
if test ${NVCC_VER} -gt 065000; then
706+
GENCODEFLAG+=' --generate-code=arch=compute_37,code=\"sm_37,compute_37\"' #K80
707+
fi
706708
fi
707709
if test ${NVCC_VER} -gt 080000; then
708710
GENCODEFLAG+=' --generate-code=arch=compute_60,code=\"sm_60,compute_60\"' #P100
@@ -1653,6 +1655,7 @@ AM_COND_IF([ANALYSIS],[AC_CONFIG_FILES([src/analysis/Makefile
16531655
src/analysis/trj_analysis/tilt_analysis/Makefile
16541656
src/analysis/trj_analysis/trj_analysis/Makefile
16551657
src/analysis/trj_analysis/ring_analysis/Makefile
1658+
src/analysis/trj_analysis/energy_analysis/Makefile
16561659
src/analysis/sp_analysis/Makefile
16571660
src/analysis/sp_analysis/libspana/Makefile
16581661
src/analysis/sp_analysis/rdf_analysis/Makefile

‎src/analysis/free_energy/pmf_analysis/pm_analyze.fpp‎

Lines changed: 17 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -195,16 +195,9 @@ contains
195195
call open_file(file_d, output%pmffile, IOFileOutputNew)
196196

197197
if (option%dimension == 1) then
198-
! Periodic CV cannot print out standard type PMF
199-
if (option%is_periodic(1)) then
200-
do i = 1, size(pmf1d(1,:))
201-
write(file_d,*) option%center(1, i), pmf1d(2, i)
202-
end do
203-
else
204-
do i = 1, size(pmf1d(1,:))
205-
write(file_d,*) option%center(1, i), pmf1d(1, i), pmf1d(2, i)
206-
end do
207-
end if
198+
do i = 1, size(pmf1d(1,:))
199+
write(file_d,*) option%center(1, i), pmf1d(1, i), pmf1d(2, i)
200+
end do
208201
else if (option%dimension == 2) then
209202

210203
if(option%output_type == OutputTypeMATLAB) then
@@ -304,14 +297,22 @@ contains
304297
do ipmf = 1, 2
305298
dx1(1:nbin, 1:ndata) = 0.0_wp
306299

307-
! Periodic CV cannot print out standard type PMF now
308-
if((ipmf == 1) .and. (option%is_periodic(1))) exit
309300
do ibin = 1, nbin
310301
if (option%is_periodic(1)) then
311-
do idata = 1, ndata
312-
dx1(ibin, idata) = (periodic(data(1, idata), option%center(1, ibin), &
313-
option%box_size(1)) / option%band_width(1))**2.0_wp
314-
end do
302+
if(ipmf == 2) then
303+
! For Gauusian type PMF
304+
do idata = 1, ndata
305+
dx1(ibin, idata) = (periodic(data(1, idata), option%center(1, ibin), &
306+
option%box_size(1)) / option%band_width(1))**2.0_wp
307+
end do
308+
else
309+
! For standard type PMF
310+
do idata = 1, ndata
311+
ddata = data(1, idata) - option%center(1, ibin)
312+
if((-option%delta_grid(1) < ddata) .and. (option%delta_grid(1) > ddata)) &
313+
dx1(ibin, idata) = dx1(ibin, idata) + 1.0_wp
314+
end do
315+
end if
315316
else
316317
if(ipmf == 2) then
317318
! For Gauusian type PMF

‎src/analysis/trj_analysis/Makefile.am‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,4 +21,5 @@ SUBDIRS = comcrd_analysis \
2121
msd_analysis \
2222
diffusion_analysis \
2323
fret_analysis \
24-
ring_analysis
24+
ring_analysis \
25+
energy_analysis

‎src/analysis/trj_analysis/energy_analysis/Makefile.am‎

Lines changed: 91 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,91 @@
1+
#--------1---------2---------3---------4---------5---------6---------7---------8
2+
#
3+
# File : Makefile.am
4+
# Authors : MK
5+
#
6+
# (c) Copyright 2016-2018 RIKEN. All rights reserved.
7+
#
8+
#--------1---------2---------3---------4---------5---------6---------7---------8
9+
if INTERNAL_LAPACK
10+
INT_LAPACK_LIB=$(LAPACK_LIB3)
11+
else
12+
INT_LAPACK_LIB=
13+
endif
14+
15+
SUBDIRS := ../../libana ../../../atdyn .
16+
17+
bin_PROGRAMS = energy_analysis
18+
19+
energy_analysis_SOURCES = \
20+
ea_option_str.fpp \
21+
ea_option.fpp \
22+
ea_control.fpp \
23+
ea_setup.fpp \
24+
ea_analyze.fpp \
25+
ea_main.fpp
26+
27+
EXTRA_DIST =\
28+
Makefile.depends
29+
30+
if QSIMULATE
31+
energy_analysis_ADDLIB = ../../../lib/lib.a ../../../lib/qsimulate/libqs.a ../../../lib/json-fortran/libjsonfortran.a
32+
else
33+
energy_analysis_ADDLIB = ../../../lib/lib.a $(INT_LAPACK_LIB)
34+
endif
35+
36+
energy_analysis_ADDLIBANA = ../../libana/libana.a
37+
optional_base = at_input.o at_boundary.o at_boundary_str.o \
38+
at_dynvars.o at_dynvars_str.o at_restraints.o \
39+
at_restraints_str.o at_remd.o at_remd_str.o \
40+
at_energy.o at_energy_angles.o at_energy_bonds.o \
41+
at_energy_dihedrals.o at_energy_go.o at_energy_nonbonds.o \
42+
at_energy_pme.o at_energy_eef1.o at_energy_gbsa.o at_energy_restraints.o \
43+
at_energy_morph.o at_energy_soft.o at_energy_cg_nonlocal.o \
44+
at_energy_str.o at_energy_table_cubic.o \
45+
at_energy_gamd.o \
46+
at_energy_table_linear.o at_energy_table_linear_bondcorr.o \
47+
at_enefunc.o at_enefunc_amber.o at_enefunc_charmm.o \
48+
at_enefunc_go.o at_enefunc_gromacs.o at_enefunc_pme.o \
49+
at_enefunc_restraints.o at_enefunc_str.o at_enefunc_gbsa.o at_enefunc_table.o \
50+
at_enefunc_gamd.o \
51+
at_experiments_str.o at_experiments.o \
52+
at_pairlist.o at_pairlist_str.o at_setup_mpi.o \
53+
at_constraints.o at_constraints_str.o at_output.o \
54+
at_md_leapfrog.o at_md_vverlet.o at_md_vverlet_cg.o at_qmmm.o \
55+
at_ensemble.o at_ensemble_str.o \
56+
at_dynamics.o at_dynamics_str.o \
57+
at_morph.o at_morph_str.o
58+
optional_objs = $(foreach file, $(optional_base), ../../../atdyn/$(file))
59+
60+
SUFFIXES = .fpp
61+
DEPENDS = Makefile.depends
62+
63+
.fpp.o:
64+
if USEKCOMP
65+
cp $*.fpp $*.f90
66+
$(FPP) $(PPFLAGS) $(DEFS) $*.f90
67+
mv $*.cpp.f90 $*.f90
68+
$(FC) $(DEFAULT_INCLUDES) $(INCLUDES) \
69+
-I../../../lib -I../../libana -I ../../../atdyn $(FCFLAGS) -c $*.f90
70+
else
71+
$(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
72+
$(FC) $(DEFAULT_INCLUDES) $(INCLUDES) \
73+
-I../../../lib -I../../libana -I ../../../atdyn $(FCFLAGS) -c $*.f90
74+
endif
75+
76+
energy_analysis$(EXEEXT) : $(energy_analysis_OBJECTS) \
77+
$(energy_analysis_ADDLIBANA) $(energy_analysis_ADDLIB)
78+
$(FC) -o $(bin_PROGRAMS) $(energy_analysis_OBJECTS) \
79+
$(optional_objs) \
80+
$(energy_analysis_ADDLIBANA) $(energy_analysis_ADDLIB) $(LDFLAGS)
81+
82+
clean:
83+
rm -f $(bin_PROGRAMS) $(energy_analysis_OBJECTS) *.f90 *~ *.mod
84+
85+
depend: clean_depend
86+
python ../../../../fortdep.py *.fpp > $(DEPENDS)
87+
88+
clean_depend:
89+
rm -f $(DEPENDS)
90+
91+
-include $(DEPENDS)

‎src/analysis/trj_analysis/energy_analysis/Makefile.depends‎

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1+
ea_analyze.o: ea_analyze.fpp ea_option_str_mod.mod
2+
ea_analyze_mod.mod: ea_analyze.fpp ea_analyze.o
3+
ea_control.o: ea_control.fpp ea_option_mod.mod
4+
ea_control_mod.mod: ea_control.fpp ea_control.o
5+
ea_main.o: ea_main.fpp ea_analyze_mod.mod ea_control_mod.mod ea_setup_mod.mod ea_option_str_mod.mod ea_option_mod.mod
6+
ea_option.o: ea_option.fpp ea_option_str_mod.mod
7+
ea_option_mod.mod: ea_option.fpp ea_option.o
8+
ea_option_str.o: ea_option_str.fpp
9+
ea_option_str_mod.mod: ea_option_str.fpp ea_option_str.o
10+
ea_setup.o: ea_setup.fpp ea_control_mod.mod ea_option_str_mod.mod ea_option_mod.mod
11+
ea_setup_mod.mod: ea_setup.fpp ea_setup.o

0 commit comments

Comments
 (0)