jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12612 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-10-07 20:30:25 +00:00
parent 3c0612815f
commit 044084847b
33 changed files with 2284 additions and 2595 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

52
lib/colvars/Makefile.fermi
View File

@ -7,18 +7,20 @@ EXTRAMAKE = Makefile.lammps.empty
# ------ SETTINGS ------
CXX = g++
CXXFLAGS = -O2 -mpc64 -march=native -funroll-loops \
-fno-rtti -fno-exceptions # -DCOLVARS_DEBUG
CXXFLAGS = -O2 -mpc64 -march=native -funroll-loops -g \
-fno-rtti -fno-exceptions -Wall -Wno-sign-compare # -DCOLVARS_DEBUG
ARCHIVE = ar
ARCHFLAG = -rscv
SHELL = /bin/sh
# ------ DEFINITIONS ------
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias.cpp colvarbias_meta.cpp \
colvar.cpp colvarcomp_angles.cpp colvarcomp.cpp colvarcomp_coordnums.cpp \
colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp \
colvargrid.cpp colvarmodule.cpp colvarparse.cpp colvarvalue.cpp
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias_alb.cpp colvarbias.cpp \
colvarbias_meta.cpp colvarbias_restraint.cpp colvarcomp_angles.cpp \
colvarcomp_coordnums.cpp colvarcomp.cpp colvarcomp_distances.cpp \
colvarcomp_protein.cpp colvarcomp_rotations.cpp colvar.cpp colvargrid.cpp \
colvarmodule.cpp colvarparse.cpp colvarscript.cpp colvartypes.cpp \
colvarvalue.cpp
LIB = libcolvars.a
OBJ = $(SRC:.cpp=.o)
@ -26,11 +28,13 @@ EXE = #colvars_standalone
# ------ MAKE PROCEDURE ------
default: $(LIB) $(EXE)
default: $(LIB) $(EXE) Makefile.lammps
Makefile.lammps:
@cp $(EXTRAMAKE) Makefile.lammps
$(LIB): $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
$(CXX) -o $@ $(CXXFLAGS) $^
@ -49,31 +53,30 @@ colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
# ------ DEPENDENCIES ------
#
colvars_main.o: colvars_main.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarproxy_standalone.h colvaratoms.h colvarparse.h colvarvalue.h
colvarproxy_standalone.o: colvarproxy_standalone.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvaratoms.h colvarparse.h colvarvalue.h \
colvarproxy_standalone.h
colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvaratoms.h
colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
colvarbias.h colvargrid.h
colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvarbias_alb.h colvar.h colvarvalue.h colvarparse.h \
colvarbias_restraint.h colvarbias.h
colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarbias.h colvar.h colvarparse.h
colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
colvarbias_meta.h colvarbias.h colvargrid.h
colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h
colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
colvarbias.h colvar.h colvarparse.h
colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
colvaratoms.h
colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
colvar.h colvarcomp.h
colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
@ -83,14 +86,23 @@ colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvarscript.h colvarbias.h
colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvargrid.h
colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvar.h colvarbias.h colvarbias_meta.h \
colvargrid.h colvarbias_abf.h
colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvarparse.h colvarvalue.h colvar.h colvarbias.h \
colvarbias_alb.h colvarbias_restraint.h colvarbias_meta.h colvargrid.h \
colvarbias_abf.h colvarscript.h
colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h
colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
colvarbias.h
colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h
colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h

43
lib/colvars/Makefile.g++
View File

@ -14,10 +14,12 @@ SHELL = /bin/sh
# ------ DEFINITIONS ------
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias.cpp colvarbias_meta.cpp \
colvar.cpp colvarcomp_angles.cpp colvarcomp.cpp colvarcomp_coordnums.cpp \
colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp \
colvargrid.cpp colvarmodule.cpp colvarparse.cpp colvarvalue.cpp colvarbias_alb.cpp
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias_alb.cpp colvarbias.cpp \
colvarbias_meta.cpp colvarbias_restraint.cpp colvarcomp_angles.cpp \
colvarcomp_coordnums.cpp colvarcomp.cpp colvarcomp_distances.cpp \
colvarcomp_protein.cpp colvarcomp_rotations.cpp colvar.cpp colvargrid.cpp \
colvarmodule.cpp colvarparse.cpp colvarscript.cpp colvartypes.cpp \
colvarvalue.cpp
LIB = libcolvars.a
OBJ = $(SRC:.cpp=.o)
@ -50,34 +52,30 @@ colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
# ------ DEPENDENCIES ------
#
colvars_main.o: colvars_main.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarproxy_standalone.h colvaratoms.h colvarparse.h colvarvalue.h
colvarproxy_standalone.o: colvarproxy_standalone.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvaratoms.h colvarparse.h colvarvalue.h \
colvarproxy_standalone.h
colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvaratoms.h
colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
colvarbias.h colvargrid.h
colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
colvar.h colvarvalue.h colvarparse.h colvarbias_alb.h \
colvarbias.h
colvarproxy.h colvarbias_alb.h colvar.h colvarvalue.h colvarparse.h \
colvarbias_restraint.h colvarbias.h
colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarbias.h colvar.h colvarparse.h
colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
colvarbias_meta.h colvarbias.h colvargrid.h
colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h
colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
colvarbias.h colvar.h colvarparse.h
colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
colvaratoms.h
colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
colvar.h colvarcomp.h
colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
@ -87,14 +85,23 @@ colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvarscript.h colvarbias.h
colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvargrid.h
colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvar.h colvarbias.h colvarbias_meta.h \
colvargrid.h colvarbias_abf.h colvarbias_alb.h
colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvarparse.h colvarvalue.h colvar.h colvarbias.h \
colvarbias_alb.h colvarbias_restraint.h colvarbias_meta.h colvargrid.h \
colvarbias_abf.h colvarscript.h
colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h
colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
colvarbias.h
colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h
colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h

42
lib/colvars/Makefile.mingw32-cross
View File

@ -17,10 +17,12 @@ SHELL = /bin/sh
# ------ DEFINITIONS ------
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias.cpp colvarbias_meta.cpp \
colvar.cpp colvarcomp_angles.cpp colvarcomp.cpp colvarcomp_coordnums.cpp \
colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp \
colvargrid.cpp colvarmodule.cpp colvarparse.cpp colvarvalue.cpp
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias_alb.cpp colvarbias.cpp \
colvarbias_meta.cpp colvarbias_restraint.cpp colvarcomp_angles.cpp \
colvarcomp_coordnums.cpp colvarcomp.cpp colvarcomp_distances.cpp \
colvarcomp_protein.cpp colvarcomp_rotations.cpp colvar.cpp colvargrid.cpp \
colvarmodule.cpp colvarparse.cpp colvarscript.cpp colvartypes.cpp \
colvarvalue.cpp
DIR = Obj_mingw32/
LIB = $(DIR)libcolvars.a
@ -58,31 +60,30 @@ $(DIR)%.o: %.cpp
# ------ DEPENDENCIES ------
#
$(DIR)colvars_main.o: colvars_main.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarproxy_standalone.h colvaratoms.h colvarparse.h colvarvalue.h
$(DIR)colvarproxy_standalone.o: colvarproxy_standalone.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvaratoms.h colvarparse.h colvarvalue.h \
colvarproxy_standalone.h
$(DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvaratoms.h
$(DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
colvarbias.h colvargrid.h
$(DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvarbias_alb.h colvar.h colvarvalue.h colvarparse.h \
colvarbias_restraint.h colvarbias.h
$(DIR)colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarbias.h colvar.h colvarparse.h
$(DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
colvarbias_meta.h colvarbias.h colvargrid.h
$(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h
$(DIR)colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
colvarbias.h colvar.h colvarparse.h
$(DIR)colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
colvaratoms.h
$(DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
$(DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
colvar.h colvarcomp.h
$(DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
$(DIR)colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
@ -92,14 +93,23 @@ $(DIR)colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h
$(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
$(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvarscript.h colvarbias.h
$(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvargrid.h
$(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvar.h colvarbias.h colvarbias_meta.h \
colvargrid.h colvarbias_abf.h
$(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvarparse.h colvarvalue.h colvar.h colvarbias.h \
colvarbias_alb.h colvarbias_restraint.h colvarbias_meta.h colvargrid.h \
colvarbias_abf.h colvarscript.h
$(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h
$(DIR)colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
colvarbias.h
$(DIR)colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h
$(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h

42
lib/colvars/Makefile.mingw64-cross
View File

@ -17,10 +17,12 @@ SHELL = /bin/sh
# ------ DEFINITIONS ------
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias.cpp colvarbias_meta.cpp \
colvar.cpp colvarcomp_angles.cpp colvarcomp.cpp colvarcomp_coordnums.cpp \
colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp \
colvargrid.cpp colvarmodule.cpp colvarparse.cpp colvarvalue.cpp
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias_alb.cpp colvarbias.cpp \
colvarbias_meta.cpp colvarbias_restraint.cpp colvarcomp_angles.cpp \
colvarcomp_coordnums.cpp colvarcomp.cpp colvarcomp_distances.cpp \
colvarcomp_protein.cpp colvarcomp_rotations.cpp colvar.cpp colvargrid.cpp \
colvarmodule.cpp colvarparse.cpp colvarscript.cpp colvartypes.cpp \
colvarvalue.cpp
DIR = Obj_mingw64/
LIB = $(DIR)libcolvars.a
@ -57,31 +59,30 @@ $(DIR)%.o: %.cpp
# ------ DEPENDENCIES ------
#
$(DIR)colvars_main.o: colvars_main.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarproxy_standalone.h colvaratoms.h colvarparse.h colvarvalue.h
$(DIR)colvarproxy_standalone.o: colvarproxy_standalone.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvaratoms.h colvarparse.h colvarvalue.h \
colvarproxy_standalone.h
$(DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvaratoms.h
$(DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
colvarbias.h colvargrid.h
$(DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvarbias_alb.h colvar.h colvarvalue.h colvarparse.h \
colvarbias_restraint.h colvarbias.h
$(DIR)colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarbias.h colvar.h colvarparse.h
$(DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
colvarbias_meta.h colvarbias.h colvargrid.h
$(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h
$(DIR)colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
colvarbias.h colvar.h colvarparse.h
$(DIR)colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
colvaratoms.h
$(DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
$(DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
colvar.h colvarcomp.h
$(DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
$(DIR)colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
@ -91,14 +92,23 @@ $(DIR)colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h
$(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
$(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvarscript.h colvarbias.h
$(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvargrid.h
$(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvar.h colvarbias.h colvarbias_meta.h \
colvargrid.h colvarbias_abf.h
$(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvarparse.h colvarvalue.h colvar.h colvarbias.h \
colvarbias_alb.h colvarbias_restraint.h colvarbias_meta.h colvargrid.h \
colvarbias_abf.h colvarscript.h
$(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h
$(DIR)colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
colvarbias.h
$(DIR)colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h
$(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h

442
lib/colvars/colvar.cpp
View File

@ -1,33 +1,31 @@
// -*- c++ -*-
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
#include "colvarscript.h"
#include <algorithm>
// XX TODO make the acf code handle forces as well as values and velocities
colvar::colvar (std::string const &conf)
{
size_t i, j;
cvm::log ("Initializing a new collective variable.\n");
get_keyval (conf, "name", this->name,
(std::string ("colvar")+cvm::to_str (cvm::colvars.size()+1)));
for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin();
cvi < cvm::colvars.end();
cvi++) {
if ((*cvi)->name == this->name)
cvm::fatal_error ("Error: this colvar cannot have the same name, \""+this->name+
"\", as another colvar.\n");
if (cvm::colvar_by_name (this->name) != NULL) {
cvm::error ("Error: this colvar cannot have the same name, \""+this->name+
"\", as another colvar.\n",
INPUT_ERROR);
}
// all tasks disabled by default
for (size_t i = 0; i < task_ntot; i++) {
for (i = 0; i < task_ntot; i++) {
tasks[i] = false;
}
@ -57,19 +55,21 @@ colvar::colvar (std::string const &conf)
cvcp->check_keywords (def_conf, def_config_key); \
cvm::decrease_depth(); \
} else { \
cvm::fatal_error ("Error: in allocating component \"" \
def_config_key"\".\n"); \
cvm::error ("Error: in allocating component \"" \
def_config_key"\".\n", \
MEMORY_ERROR); \
} \
if ( (cvcp->period != 0.0) || (cvcp->wrap_center != 0.0) ) { \
if ( (cvcp->function_type != std::string ("distance_z")) && \
(cvcp->function_type != std::string ("dihedral")) && \
(cvcp->function_type != std::string ("spin_angle")) ) { \
cvm::fatal_error ("Error: invalid use of period and/or " \
cvm::error ("Error: invalid use of period and/or " \
"wrapAround in a \""+ \
std::string (def_config_key)+ \
"\" component.\n"+ \
"Period: "+cvm::to_str(cvcp->period) + \
" wrapAround: "+cvm::to_str(cvcp->wrap_center));\
" wrapAround: "+cvm::to_str(cvcp->wrap_center), \
INPUT_ERROR); \
} \
} \
if ( ! cvcs.back()->name.size()) \
@ -120,6 +120,8 @@ colvar::colvar (std::string const &conf)
initialize_components ("orientation", "orientation", orientation);
initialize_components ("orientation "
"angle", "orientationAngle",orientation_angle);
initialize_components ("orientation "
"projection", "orientationProj",orientation_proj);
initialize_components ("tilt", "tilt", tilt);
initialize_components ("spin angle", "spinAngle", spin_angle);
@ -135,12 +137,55 @@ colvar::colvar (std::string const &conf)
"inertiaZ", inertia_z);
initialize_components ("eigenvector", "eigenvector", eigenvector);
if (!cvcs.size())
cvm::fatal_error ("Error: no valid components were provided "
"for this collective variable.\n");
if (!cvcs.size()) {
cvm::error ("Error: no valid components were provided "
"for this collective variable.\n",
INPUT_ERROR);
}
cvm::log ("All components initialized.\n");
// Setup colvar as scripted function of components
if (get_keyval (conf, "scriptedFunction", scripted_function,
"", colvarparse::parse_silent)) {
enable(task_scripted);
cvm::log("This colvar is a scripted function.");
std::string type_str;
get_keyval (conf, "scriptedFunctionType", type_str, "scalar");
x.type(colvarvalue::type_notset);
for (i = 0; i < colvarvalue::type_all; i++) {
if (type_str == colvarvalue::type_keyword[i]) {
x.type(colvarvalue::Type(i));
break;
}
}
if (x.type() == colvarvalue::type_notset) {
cvm::error("Could not parse scripted colvar type.");
return;
}
x_reported.type (x.type());
cvm::log(std::string("Expecting colvar value of type ")
+ colvarvalue::type_desc[x.type()]);
// Build ordered list of component values that will be
// passed to the script
for (i = 1; i <= cvcs.size(); i++) {
for (j = 0; j < cvcs.size(); j++) {
if (cvcs[j]->sup_np == int(i)) {
sorted_cvc_values.push_back(cvcs[j]->p_value());
break;
}
}
}
if (sorted_cvc_values.size() != cvcs.size()) {
cvm::error("Could not find order numbers for all components"
"in componentExp values.");
return;
}
}
// this is set false if any of the components has an exponent
// different from 1 in the polynomial
@ -165,7 +210,7 @@ colvar::colvar (std::string const &conf)
}
// check the available features of each cvc
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
if ((cvcs[i])->b_debug_gradients)
enable (task_gradients);
@ -198,22 +243,26 @@ colvar::colvar (std::string const &conf)
if (! (cvcs[i])->b_Jacobian_derivative)
b_Jacobian_force = false;
for (size_t j = i; j < cvcs.size(); j++) {
if ( (cvcs[i])->type() != (cvcs[j])->type() ) {
cvm::fatal_error ("ERROR: you are definining this collective variable "
"by using components of different types, \""+
colvarvalue::type_desc[(cvcs[i])->type()]+
"\" and \""+
colvarvalue::type_desc[(cvcs[j])->type()]+
"\". "
"You must use the same type in order to "
" sum them together.\n");
if (!tasks[task_scripted]) {
// If the combination of components is a scripted function,
// the components may have different types
for (size_t j = i; j < cvcs.size(); j++) {
if ( (cvcs[i])->type() != (cvcs[j])->type() ) {
cvm::log ("ERROR: you are definining this collective variable "
"by using components of different types, \""+
colvarvalue::type_desc[(cvcs[i])->type()]+
"\" and \""+
colvarvalue::type_desc[(cvcs[j])->type()]+
"\". "
"You must use the same type in order to "
" sum them together.\n");
cvm::set_error_bits(INPUT_ERROR);
}
}
}
}
{
if (!tasks[task_scripted]) {
colvarvalue::Type const value_type = (cvcs[0])->type();
if (cvm::debug())
cvm::log ("This collective variable is a "+
@ -225,8 +274,9 @@ colvar::colvar (std::string const &conf)
}
get_keyval (conf, "width", width, 1.0);
if (width <= 0.0)
cvm::fatal_error ("Error: \"width\" must be positive.\n");
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
}
lower_boundary.type (this->type());
lower_wall.type (this->type());
@ -267,19 +317,21 @@ colvar::colvar (std::string const &conf)
// consistency checks for boundaries and walls
if (tasks[task_lower_boundary] && tasks[task_upper_boundary]) {
if (lower_boundary >= upper_boundary) {
cvm::fatal_error ("Error: the upper boundary, "+
cvm::error ("Error: the upper boundary, "+
cvm::to_str (upper_boundary)+
", is not higher than the lower boundary, "+
cvm::to_str (lower_boundary)+".\n");
cvm::to_str (lower_boundary)+".\n",
INPUT_ERROR);
}
}
if (tasks[task_lower_wall] && tasks[task_upper_wall]) {
if (lower_wall >= upper_wall) {
cvm::fatal_error ("Error: the upper wall, "+
cvm::error ("Error: the upper wall, "+
cvm::to_str (upper_wall)+
", is not higher than the lower wall, "+
cvm::to_str (lower_wall)+".\n");
cvm::to_str (lower_wall)+".\n",
INPUT_ERROR);
}
if (dist2 (lower_wall, upper_wall) < 1.0E-12) {
@ -292,14 +344,16 @@ colvar::colvar (std::string const &conf)
get_keyval (conf, "expandBoundaries", expand_boundaries, false);
if (expand_boundaries && periodic_boundaries()) {
cvm::fatal_error ("Error: trying to expand boundaries that already "
"cover a whole period of a periodic colvar.\n");
cvm::error ("Error: trying to expand boundaries that already "
"cover a whole period of a periodic colvar.\n",
INPUT_ERROR);
}
if (expand_boundaries && hard_lower_boundary && hard_upper_boundary) {
cvm::fatal_error ("Error: inconsistent configuration "
cvm::error ("Error: inconsistent configuration "
"(trying to expand boundaries with both "
"hardLowerBoundary and hardUpperBoundary enabled).\n");
}
"hardLowerBoundary and hardUpperBoundary enabled).\n",
INPUT_ERROR);
}
{
bool b_extended_lagrangian;
@ -320,21 +374,24 @@ colvar::colvar (std::string const &conf)
const bool found = get_keyval (conf, "extendedTemp", temp, cvm::temperature());
if (temp <= 0.0) {
if (found)
cvm::fatal_error ("Error: \"extendedTemp\" must be positive.\n");
cvm::log ("Error: \"extendedTemp\" must be positive.\n");
else
cvm::fatal_error ("Error: a positive temperature must be provided, either "
"by enabling a thermostat, or through \"extendedTemp\".\n");
cvm::error ("Error: a positive temperature must be provided, either "
"by enabling a thermostat, or through \"extendedTemp\".\n",
INPUT_ERROR);
}
get_keyval (conf, "extendedFluctuation", tolerance, width);
if (tolerance <= 0.0)
cvm::fatal_error ("Error: \"extendedFluctuation\" must be positive.\n");
get_keyval (conf, "extendedFluctuation", tolerance);
if (tolerance <= 0.0) {
cvm::error("Error: \"extendedFluctuation\" must be positive.\n", INPUT_ERROR);
}
ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
cvm::log ("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " kcal/mol/U^2");
get_keyval (conf, "extendedTimeConstant", period, 200.0);
if (period <= 0.0)
cvm::fatal_error ("Error: \"extendedTimeConstant\" must be positive.\n");
if (period <= 0.0) {
cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", INPUT_ERROR);
}
ext_mass = (cvm::boltzmann() * temp * period * period)
/ (4.0 * PI * PI * tolerance * tolerance);
cvm::log ("Computed fictitious mass: " + cvm::to_str(ext_mass) + " kcal/mol/(U/fs)^2 (U: colvar unit)");
@ -348,8 +405,9 @@ colvar::colvar (std::string const &conf)
}
get_keyval (conf, "extendedLangevinDamping", ext_gamma, 1.0);
if (ext_gamma < 0.0)
cvm::fatal_error ("Error: \"extendedLangevinDamping\" may not be negative.\n");
if (ext_gamma < 0.0) {
cvm::error("Error: \"extendedLangevinDamping\" may not be negative.\n", INPUT_ERROR);
}
if (ext_gamma != 0.0) {
enable (task_langevin);
ext_gamma *= 1.0e-3; // convert from ps-1 to fs-1
@ -414,7 +472,15 @@ void colvar::build_atom_list (void)
temp_id_list.sort();
temp_id_list.unique();
atom_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
// atom_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
unsigned int id_i = 0;
std::list<int>::iterator li;
for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) {
atom_ids[id_i] = *li;
id_i++;
}
temp_id_list.clear();
atomic_gradients.resize (atom_ids.size());
@ -427,7 +493,7 @@ void colvar::build_atom_list (void)
}
void colvar::parse_analysis (std::string const &conf)
int colvar::parse_analysis (std::string const &conf)
{
// if (cvm::debug())
@ -443,8 +509,9 @@ void colvar::parse_analysis (std::string const &conf)
get_keyval (conf, "runAveLength", runave_length, 1000);
get_keyval (conf, "runAveStride", runave_stride, 1);
if ((cvm::restart_out_freq % runave_stride) != 0)
cvm::fatal_error ("Error: runAveStride must be commensurate with the restart frequency.\n");
if ((cvm::restart_out_freq % runave_stride) != 0) {
cvm::error("Error: runAveStride must be commensurate with the restart frequency.\n", INPUT_ERROR);
}
std::string runave_outfile;
get_keyval (conf, "runAveOutputFile", runave_outfile,
@ -484,30 +551,33 @@ void colvar::parse_analysis (std::string const &conf)
acf_type = acf_vel;
enable (task_fdiff_velocity);
if (acf_colvar_name.size())
(cvm::colvar_p (acf_colvar_name))->enable (task_fdiff_velocity);
(cvm::colvar_by_name (acf_colvar_name))->enable (task_fdiff_velocity);
} else if (acf_type_str == to_lower_cppstr (std::string ("coordinate_p2"))) {
acf_type = acf_p2coor;
} else {
cvm::fatal_error ("Unknown type of correlation function, \""+
cvm::log ("Unknown type of correlation function, \""+
acf_type_str+"\".\n");
cvm::set_error_bits(INPUT_ERROR);
}
get_keyval (conf, "corrFuncOffset", acf_offset, 0);
get_keyval (conf, "corrFuncLength", acf_length, 1000);
get_keyval (conf, "corrFuncStride", acf_stride, 1);
if ((cvm::restart_out_freq % acf_stride) != 0)
cvm::fatal_error ("Error: corrFuncStride must be commensurate with the restart frequency.\n");
if ((cvm::restart_out_freq % acf_stride) != 0) {
cvm::error("Error: corrFuncStride must be commensurate with the restart frequency.\n", INPUT_ERROR);
}
get_keyval (conf, "corrFuncNormalize", acf_normalize, true);
get_keyval (conf, "corrFuncOutputFile", acf_outfile,
std::string (cvm::output_prefix+"."+this->name+
".corrfunc.dat"));
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void colvar::enable (colvar::task const &t)
int colvar::enable (colvar::task const &t)
{
switch (t) {
@ -528,13 +598,17 @@ void colvar::enable (colvar::task const &t)
if ( !tasks[task_extended_lagrangian] ) {
enable (task_gradients);
if (!b_Jacobian_force)
cvm::fatal_error ("Error: colvar \""+this->name+
"\" does not have Jacobian forces implemented.\n");
if (!b_linear)
cvm::fatal_error ("Error: colvar \""+this->name+
if (!b_Jacobian_force) {
cvm::error ("Error: colvar \""+this->name+
"\" does not have Jacobian forces implemented.\n",
INPUT_ERROR);
}
if (!b_linear) {
cvm::error ("Error: colvar \""+this->name+
"\" must be defined as a linear combination "
"to calculate the Jacobian force.\n");
"to calculate the Jacobian force.\n",
INPUT_ERROR);
}
if (cvm::debug())
cvm::log ("Enabling calculation of the Jacobian force "
"on this colvar.\n");
@ -545,9 +619,10 @@ void colvar::enable (colvar::task const &t)
case task_system_force:
if (!tasks[task_extended_lagrangian]) {
if (!b_inverse_gradients) {
cvm::fatal_error ("Error: one or more of the components of "
cvm::error ("Error: one or more of the components of "
"colvar \""+this->name+
"\" does not support system force calculation.\n");
"\" does not support system force calculation.\n",
INPUT_ERROR);
}
cvm::request_system_force();
}
@ -573,9 +648,11 @@ void colvar::enable (colvar::task const &t)
break;
case task_grid:
if (this->type() != colvarvalue::type_scalar)
cvm::fatal_error ("Cannot calculate a grid for collective variable, \""+
this->name+"\", because its value is not a scalar number.\n");
if (this->type() != colvarvalue::type_scalar) {
cvm::error ("Cannot calculate a grid for collective variable, \""+
this->name+"\", because its value is not a scalar number.\n",
INPUT_ERROR);
}
break;
case task_extended_lagrangian:
@ -586,8 +663,9 @@ void colvar::enable (colvar::task const &t)
case task_lower_boundary:
case task_upper_boundary:
if (this->type() != colvarvalue::type_scalar) {
cvm::fatal_error ("Error: this colvar is not a scalar value "
"and cannot produce a grid.\n");
cvm::error ("Error: this colvar is not a scalar value "
"and cannot produce a grid.\n",
INPUT_ERROR);
}
break;
@ -597,6 +675,7 @@ void colvar::enable (colvar::task const &t)
case task_ntot:
case task_langevin:
case task_output_energy:
case task_scripted:
break;
case task_gradients:
@ -605,19 +684,21 @@ void colvar::enable (colvar::task const &t)
break;
case task_collect_gradients:
if (this->type() != colvarvalue::type_scalar)
cvm::fatal_error ("Collecting atomic gradients for non-scalar collective variable \""+
this->name+"\" is not yet implemented.\n");
if (this->type() != colvarvalue::type_scalar) {
cvm::error ("Collecting atomic gradients for non-scalar collective variable \""+
this->name+"\" is not yet implemented.\n",
INPUT_ERROR);
}
enable (task_gradients);
if (atom_ids.size() == 0) {
build_atom_list();
}
break;
}
tasks[t] = true;
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -665,6 +746,7 @@ void colvar::disable (colvar::task const &t)
case task_langevin:
case task_output_energy:
case task_collect_gradients:
case task_scripted:
break;
}
@ -689,6 +771,16 @@ colvar::~colvar()
for (size_t i = 0; i < cvcs.size(); i++) {
delete cvcs[i];
}
// remove reference to this colvar from the CVM
for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin();
cvi != cvm::colvars.end();
++cvi) {
if ( *cvi == this) {
cvm::colvars.erase (cvi);
break;
}
}
}
@ -698,14 +790,15 @@ colvar::~colvar()
void colvar::calc()
{
size_t i, ig;
if (cvm::debug())
cvm::log ("Calculating colvar \""+this->name+"\".\n");
// prepare atom groups for calculation
if (cvm::debug())
cvm::log ("Collecting data from atom groups.\n");
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
atoms.reset_atoms_data();
atoms.read_positions();
@ -716,15 +809,15 @@ void colvar::calc()
}
}
if (tasks[task_output_velocity]) {
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvcs[i]->atom_groups[ig]->read_velocities();
}
}
}
if (tasks[task_system_force]) {
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvcs[i]->atom_groups[ig]->read_system_forces();
}
}
@ -735,35 +828,42 @@ void colvar::calc()
if (cvm::debug())
cvm::log ("Calculating colvar components.\n");
x.reset();
if (x.type() == colvarvalue::type_scalar) {
// polynomial combination allowed
for (size_t i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->calc_value();
cvm::decrease_depth();
if (cvm::debug())
cvm::log ("Colvar component no. "+cvm::to_str (i+1)+
" within colvar \""+this->name+"\" has value "+
cvm::to_str ((cvcs[i])->value(),
cvm::cv_width, cvm::cv_prec)+".\n");
// First, update component values
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->calc_value();
cvm::decrease_depth();
if (cvm::debug())
cvm::log ("Colvar component no. "+cvm::to_str (i+1)+
" within colvar \""+this->name+"\" has value "+
cvm::to_str ((cvcs[i])->value(),
cvm::cv_width, cvm::cv_prec)+".\n");
}
// Then combine them appropriately
if (tasks[task_scripted]) {
// cvcs combined by user script
int res = cvm::proxy->run_colvar_callback(scripted_function, sorted_cvc_values, x);
if (res == COLVARS_NOT_IMPLEMENTED) {
cvm::error("Scripted colvars are not implemented.");
return;
}
if (res != COLVARS_OK) {
cvm::error("Error running scripted colvar");
return;
}
} else if (x.type() == colvarvalue::type_scalar) {
// polynomial combination allowed
for (i = 0; i < cvcs.size(); i++) {
x += (cvcs[i])->sup_coeff *
( ((cvcs[i])->sup_np != 1) ?
std::pow ((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
(cvcs[i])->value().real_value );
( ((cvcs[i])->sup_np != 1) ?
std::pow ((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
(cvcs[i])->value().real_value );
}
} else {
// only linear combination allowed
for (size_t i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->calc_value();
cvm::decrease_depth();
if (cvm::debug())
cvm::log ("Colvar component no. "+cvm::to_str (i+1)+
" within colvar \""+this->name+"\" has value "+
cvm::to_str ((cvcs[i])->value(),
cvm::cv_width, cvm::cv_prec)+".\n");
for (i = 0; i < cvcs.size(); i++) {
x += (cvcs[i])->sup_coeff * (cvcs[i])->value();
}
}
@ -777,7 +877,7 @@ void colvar::calc()
if (cvm::debug())
cvm::log ("Calculating gradients of colvar \""+this->name+"\".\n");
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
// calculate the gradients of each component
cvm::increase_depth();
@ -785,7 +885,7 @@ void colvar::calc()
// if requested, propagate (via chain rule) the gradients above
// to the atoms used to define the roto-translation
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
if (cvcs[i]->atom_groups[ig]->b_fit_gradients)
cvcs[i]->atom_groups[ig]->calc_fit_gradients();
}
@ -797,11 +897,18 @@ void colvar::calc()
cvm::log ("Done calculating gradients of colvar \""+this->name+"\".\n");
if (tasks[task_collect_gradients]) {
if (tasks[task_scripted]) {
cvm::error("Collecting atomic gradients is not implemented for "
"scripted colvars.");
return;
}
// Collect the atomic gradients inside colvar object
for (int a = 0; a < atomic_gradients.size(); a++) {
for (unsigned int a = 0; a < atomic_gradients.size(); a++) {
atomic_gradients[a].reset();
}
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
// Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real ((cvcs[i])->sup_np) *
std::pow ((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);
@ -835,14 +942,25 @@ void colvar::calc()
if (tasks[task_system_force]) {
if (tasks[task_scripted]) {
// TODO see if this could reasonably be done in a generic way
// from generic inverse gradients
cvm::error("System force is not implemented for "
"scripted colvars.");
return;
}
if (cvm::debug())
cvm::log ("Calculating system force of colvar \""+this->name+"\".\n");
ft.reset();
if(!tasks[task_extended_lagrangian] && (cvm::step_relative() > 0)) {
// if(!tasks[task_extended_lagrangian] && (cvm::step_relative() > 0)) {
// Disabled check to allow for explicit system force calculation
// even with extended Lagrangian
if(cvm::step_relative() > 0) {
// get from the cvcs the system forces from the PREVIOUS step
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
(cvcs[i])->calc_force_invgrads();
// linear combination is assumed
cvm::increase_depth();
@ -949,15 +1067,15 @@ cvm::real colvar::update()
}
if (tasks[task_Jacobian_force]) {
size_t i;
cvm::increase_depth();
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
(cvcs[i])->calc_Jacobian_derivative();
}
cvm::decrease_depth();
fj.reset();
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
// linear combination is assumed
fj += 1.0 / ( cvm::real (cvcs.size()) * cvm::real ((cvcs[i])->sup_coeff) ) *
(cvcs[i])->Jacobian_derivative();
@ -1016,12 +1134,32 @@ cvm::real colvar::update()
void colvar::communicate_forces()
{
size_t i;
if (cvm::debug())
cvm::log ("Communicating forces from colvar \""+this->name+"\".\n");
if (x.type() == colvarvalue::type_scalar) {
if (tasks[task_scripted]) {
std::vector<colvarvalue> func_grads(cvcs.size());
int res = cvm::proxy->run_colvar_gradient_callback(scripted_function, sorted_cvc_values, func_grads);
for (size_t i = 0; i < cvcs.size(); i++) {
if (res == COLVARS_NOT_IMPLEMENTED) {
cvm::error("Colvar gradient scripts are not implemented.");
return;
}
if (res != COLVARS_OK) {
cvm::error("Error running colvar gradient script");
return;
}
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
// Note: we need a dot product here
(cvcs[i])->apply_force (f * func_grads[i]);
cvm::decrease_depth();
}
} else if (x.type() == colvarvalue::type_scalar) {
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->apply_force (f * (cvcs[i])->sup_coeff *
cvm::real ((cvcs[i])->sup_np) *
@ -1032,7 +1170,7 @@ void colvar::communicate_forces()
} else {
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->apply_force (f * (cvcs[i])->sup_coeff);
cvm::decrease_depth();
@ -1052,10 +1190,11 @@ void colvar::communicate_forces()
bool colvar::periodic_boundaries (colvarvalue const &lb, colvarvalue const &ub) const
{
if ( (!tasks[task_lower_boundary]) || (!tasks[task_upper_boundary]) ) {
cvm::fatal_error ("Error: requesting to histogram the "
cvm::log ("Error: requesting to histogram the "
"collective variable \""+this->name+"\", but a "
"pair of lower and upper boundaries must be "
"defined.\n");
cvm::set_error_bits(INPUT_ERROR);
}
if (period > 0.0) {
@ -1071,7 +1210,7 @@ bool colvar::periodic_boundaries (colvarvalue const &lb, colvarvalue const &ub)
bool colvar::periodic_boundaries() const
{
if ( (!tasks[task_lower_boundary]) || (!tasks[task_upper_boundary]) ) {
cvm::fatal_error ("Error: requesting to histogram the "
cvm::error ("Error: requesting to histogram the "
"collective variable \""+this->name+"\", but a "
"pair of lower and upper boundaries must be "
"defined.\n");
@ -1132,11 +1271,11 @@ std::istream & colvar::read_restart (std::istream &is)
if ( (get_keyval (conf, "name", check_name,
std::string (""), colvarparse::parse_silent)) &&
(check_name != name) ) {
cvm::fatal_error ("Error: the state file does not match the "
cvm::error ("Error: the state file does not match the "
"configuration file, at colvar \""+name+"\".\n");
}
if (check_name.size() == 0) {
cvm::fatal_error ("Error: Collective variable in the "
cvm::error ("Error: Collective variable in the "
"restart file without any identifier.\n");
}
}
@ -1383,7 +1522,7 @@ std::ostream & colvar::write_traj (std::ostream &os)
return os;
}
void colvar::write_output_files()
int colvar::write_output_files()
{
if (cvm::b_analysis) {
@ -1391,8 +1530,9 @@ void colvar::write_output_files()
cvm::log ("Writing acf to file \""+acf_outfile+"\".\n");
std::ofstream acf_os (acf_outfile.c_str());
if (! acf_os.good())
cvm::fatal_error ("Cannot open file \""+acf_outfile+"\".\n");
if (! acf_os.good()) {
cvm::error("Cannot open file \""+acf_outfile+"\".\n", FILE_ERROR);
}
write_acf (acf_os);
acf_os.close();
}
@ -1401,6 +1541,7 @@ void colvar::write_output_files()
runave_os.close();
}
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -1436,7 +1577,7 @@ inline void history_incr (std::list< std::list<colvarvalue> > &history
}
void colvar::calc_acf()
int colvar::calc_acf()
{
// using here an acf_stride-long list of vectors for either
// coordinates (acf_x_history) or velocities (acf_v_history); each vector can
@ -1444,17 +1585,19 @@ void colvar::calc_acf()
// representation but separated by acf_stride in the time series;
// the pointer to each vector is changed at every step
if (! (acf_x_history.size() || acf_v_history.size()) ) {
if (acf_x_history.empty() && acf_v_history.empty()) {
// first-step operations
colvar *cfcv = (acf_colvar_name.size() ?
cvm::colvar_p (acf_colvar_name) :
cvm::colvar_by_name (acf_colvar_name) :
this);
if (cfcv->type() != this->type())
cvm::fatal_error ("Error: correlation function between \""+cfcv->name+
if (cfcv->type() != this->type()) {
cvm::error ("Error: correlation function between \""+cfcv->name+
"\" and \""+this->name+"\" cannot be calculated, "
"because their value types are different.\n");
"because their value types are different.\n",
INPUT_ERROR);
}
acf_nframes = 0;
cvm::log ("Colvar \""+this->name+"\": initializing ACF calculation.\n");
@ -1462,11 +1605,12 @@ void colvar::calc_acf()
if (acf.size() < acf_length+1)
acf.resize (acf_length+1, 0.0);
size_t i;
switch (acf_type) {
case acf_vel:
// allocate space for the velocities history
for (size_t i = 0; i < acf_stride; i++) {
for (i = 0; i < acf_stride; i++) {
acf_v_history.push_back (std::list<colvarvalue>());
}
acf_v_history_p = acf_v_history.begin();
@ -1475,7 +1619,7 @@ void colvar::calc_acf()
case acf_coor:
case acf_p2coor:
// allocate space for the coordinates history
for (size_t i = 0; i < acf_stride; i++) {
for (i = 0; i < acf_stride; i++) {
acf_x_history.push_back (std::list<colvarvalue>());
}
acf_x_history_p = acf_x_history.begin();
@ -1488,7 +1632,7 @@ void colvar::calc_acf()
} else {
colvar *cfcv = (acf_colvar_name.size() ?
cvm::colvar_p (acf_colvar_name) :
cvm::colvar_by_name (acf_colvar_name) :
this);
switch (acf_type) {
@ -1532,10 +1676,11 @@ void colvar::calc_acf()
// set it for the next step
x_old = x;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
int colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
colvarvalue const &v)
{
// loop over stored velocities and add to the ACF, but only the
@ -1545,10 +1690,11 @@ void colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
vs_i++;
++vs_i;
// current vel with itself
*(acf_i++) += v.norm2();
*(acf_i) += v.norm2();
++acf_i;
// inner products of previous velocities with current (acf_i and
// vs_i are updated)
@ -1556,6 +1702,7 @@ void colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
acf_nframes++;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -1568,7 +1715,7 @@ void colvar::calc_coor_acf (std::list<colvarvalue> &x_list,
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
xs_i++;
++xs_i;
*(acf_i++) += x.norm2();
@ -1589,7 +1736,7 @@ void colvar::calc_p2coor_acf (std::list<colvarvalue> &x_list,
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
xs_i++;
++xs_i;
// value of P2(0) = 1
*(acf_i++) += 1.0;
@ -1617,7 +1764,7 @@ void colvar::write_acf (std::ostream &os)
cvm::real const acf_norm = acf.front() / cvm::real (acf_nframes);
std::vector<cvm::real>::iterator acf_i;
size_t it = acf_offset;
for (acf_i = acf.begin(); acf_i != acf.end(); acf_i++) {
for (acf_i = acf.begin(); acf_i != acf.end(); ++acf_i) {
os << std::setw (cvm::it_width) << acf_stride * (it++) << " "
<< std::setprecision (cvm::cv_prec)
<< std::setw (cvm::cv_width)
@ -1630,7 +1777,7 @@ void colvar::write_acf (std::ostream &os)
void colvar::calc_runave()
{
if (!x_history.size()) {
if (x_history.empty()) {
runave.type (x.type());
runave.reset();
@ -1653,8 +1800,9 @@ void colvar::calc_runave()
if ((*x_history_p).size() >= runave_length-1) {
runave = x;
for (std::list<colvarvalue>::iterator xs_i = (*x_history_p).begin();
xs_i != (*x_history_p).end(); xs_i++) {
std::list<colvarvalue>::iterator xs_i;
for (xs_i = (*x_history_p).begin();
xs_i != (*x_history_p).end(); ++xs_i) {
runave += (*xs_i);
}
runave *= 1.0 / cvm::real (runave_length);
@ -1662,8 +1810,8 @@ void colvar::calc_runave()
runave_variance = 0.0;
runave_variance += this->dist2 (x, runave);
for (std::list<colvarvalue>::iterator xs_i = (*x_history_p).begin();
xs_i != (*x_history_p).end(); xs_i++) {
for (xs_i = (*x_history_p).begin();
xs_i != (*x_history_p).end(); ++xs_i) {
runave_variance += this->dist2 (x, (*xs_i));
}
runave_variance *= 1.0 / cvm::real (runave_length-1);

39
lib/colvars/colvar.h
View File

@ -1,4 +1,4 @@
// -*- c++ -*-
/// -*- c++ -*-
#ifndef COLVAR_H
#define COLVAR_H
@ -148,6 +148,8 @@ public:
task_runave,
/// \brief Compute time correlation function
task_corrfunc,
/// \brief Value and gradients computed by user script
task_scripted,
/// \brief Number of possible tasks
task_ntot
};
@ -155,6 +157,8 @@ public:
/// Tasks performed by this colvar
bool tasks[task_ntot];
/// List of biases that depend on this colvar
std::vector<colvarbias *> biases;
protected:
@ -283,7 +287,7 @@ public:
colvar (std::string const &conf);
/// Enable the specified task
void enable (colvar::task const &t);
int enable (colvar::task const &t);
/// Disable the specified task
void disable (colvar::task const &t);
@ -355,7 +359,7 @@ public:
/// Read the analysis tasks
void parse_analysis (std::string const &conf);
int parse_analysis (std::string const &conf);
/// Perform analysis tasks
void analyse();
@ -374,7 +378,7 @@ public:
std::ostream & write_restart (std::ostream &os);
/// Write output files (if defined, e.g. in analysis mode)
void write_output_files();
int write_output_files();
protected:
@ -430,7 +434,7 @@ protected:
acf_type_e acf_type;
/// \brief Velocity ACF, scalar product between v(0) and v(t)
void calc_vel_acf (std::list<colvarvalue> &v_history,
int calc_vel_acf (std::list<colvarvalue> &v_history,
colvarvalue const &v);
/// \brief Coordinate ACF, scalar product between x(0) and x(t)
@ -444,7 +448,7 @@ protected:
colvarvalue const &x);
/// Calculate the auto-correlation function (ACF)
void calc_acf();
int calc_acf();
/// Save the ACF to a file
void write_acf (std::ostream &os);
@ -485,6 +489,7 @@ public:
class h_bond;
class rmsd;
class orientation_angle;
class orientation_proj;
class tilt;
class spin_angle;
class gyration;
@ -509,6 +514,14 @@ protected:
/// in all cvcs (called when enabling task_collect_gradients)
void build_atom_list (void);
private:
/// Name of scripted function to be used
std::string scripted_function;
/// Current cvc values in the order requested by script
/// when using scriptedFunction
std::vector<const colvarvalue *> sorted_cvc_values;
public:
/// \brief Sorted array of (zero-based) IDs for all atoms involved
std::vector<int> atom_ids;
@ -523,20 +536,6 @@ public:
}
};
inline colvar * cvm::colvar_p (std::string const &name)
{
for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin();
cvi != cvm::colvars.end();
cvi++) {
if ((*cvi)->name == name) {
return (*cvi);
}
}
return NULL;
}
inline colvarvalue::Type colvar::type() const
{
return x.type();

222
lib/colvars/colvaratoms.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarparse.h"
#include "colvaratoms.h"
@ -44,8 +46,8 @@ cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
cvm::atom_group::atom_group()
: b_dummy (false), b_center (false), b_rotate (false),
b_fit_gradients (false), ref_pos_group (NULL),
noforce (false)
b_user_defined_fit (false), b_fit_gradients (false),
ref_pos_group (NULL), noforce (false)
{
total_mass = 0.0;
}
@ -63,7 +65,7 @@ cvm::atom_group::~atom_group()
void cvm::atom_group::add_atom (cvm::atom const &a)
{
if (b_dummy) {
cvm::fatal_error ("Error: cannot add atoms to a dummy group.\n");
cvm::error ("Error: cannot add atoms to a dummy group.\n", INPUT_ERROR);
} else {
this->push_back (a);
total_mass += a.mass;
@ -83,7 +85,7 @@ void cvm::atom_group::reset_mass(std::string &name, int i, int j)
" atoms: total mass = "+cvm::to_str (this->total_mass)+".\n");
}
void cvm::atom_group::parse (std::string const &conf,
int cvm::atom_group::parse (std::string const &conf,
char const *key)
{
std::string group_conf;
@ -98,9 +100,10 @@ void cvm::atom_group::parse (std::string const &conf,
save_delimiters = true;
if (group_conf.size() == 0) {
cvm::fatal_error ("Error: atom group \""+
std::string (key)+"\" is set, but "
"has no definition.\n");
cvm::error ("Error: atom group \""+std::string (key)+
"\" is set, but has no definition.\n",
INPUT_ERROR);
return COLVARS_ERROR;
}
cvm::increase_depth();
@ -135,9 +138,11 @@ void cvm::atom_group::parse (std::string const &conf,
for (size_t i = 0; i < atom_indexes.size(); i++) {
this->push_back (cvm::atom (atom_indexes[i]));
}
} else
cvm::fatal_error ("Error: no numbers provided for \""
"atomNumbers\".\n");
} else {
cvm::error ("Error: no numbers provided for \""
"atomNumbers\".\n", INPUT_ERROR);
return COLVARS_ERROR;
}
atom_indexes.clear();
}
@ -147,13 +152,15 @@ void cvm::atom_group::parse (std::string const &conf,
// use an index group from the index file read globally
std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
std::list<std::vector<int> >::iterator index_groups_i = cvm::index_groups.begin();
for ( ; names_i != cvm::index_group_names.end() ; names_i++, index_groups_i++) {
for ( ; names_i != cvm::index_group_names.end() ; ++names_i, ++index_groups_i) {
if (*names_i == index_group_name)
break;
}
if (names_i == cvm::index_group_names.end()) {
cvm::fatal_error ("Error: could not find index group "+
index_group_name+" among those provided by the index file.\n");
cvm::error ("Error: could not find index group "+
index_group_name+" among those provided by the index file.\n",
INPUT_ERROR);
return COLVARS_ERROR;
}
this->reserve (index_groups_i->size());
for (size_t i = 0; i < index_groups_i->size(); i++) {
@ -183,20 +190,19 @@ void cvm::atom_group::parse (std::string const &conf,
}
}
cvm::fatal_error ("Error: no valid definition for \""
"atomNumbersRange\", \""+
range_conf+"\".\n");
cvm::error ("Error: no valid definition for \"atomNumbersRange\", \""+
range_conf+"\".\n", INPUT_ERROR);
}
}
std::vector<std::string> psf_segids;
get_keyval (group_conf, "psfSegID", psf_segids, std::vector<std::string> (), mode);
for (std::vector<std::string>::iterator psii = psf_segids.begin();
psii < psf_segids.end(); psii++) {
psii < psf_segids.end(); ++psii) {
if ( (psii->size() == 0) || (psii->size() > 4) ) {
cvm::fatal_error ("Error: invalid segmend identifier provided, \""+
(*psii)+"\".\n");
cvm::error ("Error: invalid segmend identifier provided, \""+
(*psii)+"\".\n", INPUT_ERROR);
}
}
@ -210,8 +216,8 @@ void cvm::atom_group::parse (std::string const &conf,
range_count++;
if (range_count > psf_segids.size()) {
cvm::fatal_error ("Error: more instances of \"atomNameResidueRange\" than "
"values of \"psfSegID\".\n");
cvm::error ("Error: more instances of \"atomNameResidueRange\" than "
"values of \"psfSegID\".\n", INPUT_ERROR);
}
std::string const &psf_segid = psf_segids.size() ? *psii : std::string ("");
@ -231,17 +237,17 @@ void cvm::atom_group::parse (std::string const &conf,
}
range_conf = "";
} else {
cvm::fatal_error ("Error: cannot parse definition for \""
"atomNameResidueRange\", \""+
range_conf+"\".\n");
cvm::error ("Error: cannot parse definition for \""
"atomNameResidueRange\", \""+
range_conf+"\".\n");
}
} else {
cvm::fatal_error ("Error: atomNameResidueRange with empty definition.\n");
cvm::error ("Error: atomNameResidueRange with empty definition.\n");
}
if (psf_segid.size())
psii++;
++psii;
}
}
@ -252,24 +258,25 @@ void cvm::atom_group::parse (std::string const &conf,
std::string atoms_col;
if (!get_keyval (group_conf, "atomsCol", atoms_col, std::string (""), mode)) {
cvm::fatal_error ("Error: parameter atomsCol is required if atomsFile is set.\n");
cvm::error ("Error: parameter atomsCol is required if atomsFile is set.\n",
INPUT_ERROR);
}
double atoms_col_value;
bool const atoms_col_value_defined = get_keyval (group_conf, "atomsColValue", atoms_col_value, 0.0, mode);
if (atoms_col_value_defined && (!atoms_col_value))
cvm::fatal_error ("Error: atomsColValue, "
"if provided, must be non-zero.\n");
if (atoms_col_value_defined && (!atoms_col_value)) {
cvm::error ("Error: atomsColValue, if provided, must be non-zero.\n", INPUT_ERROR);
}
cvm::load_atoms (atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
}
}
for (std::vector<cvm::atom>::iterator a1 = this->begin();
a1 != this->end(); a1++) {
a1 != this->end(); ++a1) {
std::vector<cvm::atom>::iterator a2 = a1;
++a2;
for ( ; a2 != this->end(); a2++) {
for ( ; a2 != this->end(); ++a2) {
if (a1->id == a2->id) {
if (cvm::debug())
cvm::log ("Discarding doubly counted atom with number "+
@ -287,14 +294,15 @@ void cvm::atom_group::parse (std::string const &conf,
} else
b_dummy = false;
if (b_dummy && (this->size()))
cvm::fatal_error ("Error: cannot set up group \""+
std::string (key)+"\" as a dummy atom "
"and provide it with atom definitions.\n");
if (b_dummy && (this->size())) {
cvm::error ("Error: cannot set up group \""+
std::string (key)+"\" as a dummy atom "
"and provide it with atom definitions.\n", INPUT_ERROR);
}
#if (! defined (COLVARS_STANDALONE))
if ( (!b_dummy) && (!cvm::b_analysis) && (!(this->size())) ) {
cvm::fatal_error ("Error: no atoms defined for atom group \""+
cvm::error ("Error: no atoms defined for atom group \""+
std::string (key)+"\".\n");
}
#endif
@ -329,17 +337,17 @@ void cvm::atom_group::parse (std::string const &conf,
if (b_center || b_rotate) {
if (b_dummy)
cvm::fatal_error ("Error: centerReference or rotateReference "
"cannot be defined for a dummy atom.\n");
cvm::error ("Error: centerReference or rotateReference "
"cannot be defined for a dummy atom.\n");
if (key_lookup (group_conf, "refPositionsGroup")) {
// instead of this group, define another group to compute the fit
if (ref_pos_group) {
cvm::fatal_error ("Error: the atom group \""+
std::string (key)+"\" has already a reference group "
"for the rototranslational fit, which was communicated by the "
"colvar component. You should not use refPositionsGroup "
"in this case.\n");
cvm::error ("Error: the atom group \""+
std::string (key)+"\" has already a reference group "
"for the rototranslational fit, which was communicated by the "
"colvar component. You should not use refPositionsGroup "
"in this case.\n");
}
cvm::log ("Within atom group \""+std::string (key)+"\":\n");
ref_pos_group = new atom_group (group_conf, "refPositionsGroup");
@ -357,8 +365,8 @@ void cvm::atom_group::parse (std::string const &conf,
if (get_keyval (group_conf, "refPositionsFile", ref_pos_file, std::string (""), mode)) {
if (ref_pos.size()) {
cvm::fatal_error ("Error: cannot specify \"refPositionsFile\" and "
"\"refPositions\" at the same time.\n");
cvm::error ("Error: cannot specify \"refPositionsFile\" and "
"\"refPositions\" at the same time.\n");
}
std::string ref_pos_col;
@ -368,8 +376,8 @@ void cvm::atom_group::parse (std::string const &conf,
// if provided, use PDB column to select coordinates
bool found = get_keyval (group_conf, "refPositionsColValue", ref_pos_col_value, 0.0, mode);
if (found && !ref_pos_col_value)
cvm::fatal_error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
cvm::error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
} else {
// if not, rely on existing atom indices for the group
group_for_fit->create_sorted_ids();
@ -384,13 +392,13 @@ void cvm::atom_group::parse (std::string const &conf,
if (b_rotate) {
if (ref_pos.size() != group_for_fit->size())
cvm::fatal_error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms within \""+
std::string (key)+
"\" ("+cvm::to_str (group_for_fit->size())+
"): to perform a rotational fit, "+
"these numbers should be equal.\n");
cvm::error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms within \""+
std::string (key)+
"\" ("+cvm::to_str (group_for_fit->size())+
"): to perform a rotational fit, "+
"these numbers should be equal.\n", INPUT_ERROR);
}
// save the center of geometry of ref_pos and subtract it
@ -398,7 +406,7 @@ void cvm::atom_group::parse (std::string const &conf,
} else {
#if (! defined (COLVARS_STANDALONE))
cvm::fatal_error ("Error: no reference positions provided.\n");
cvm::error ("Error: no reference positions provided.\n");
#endif
}
@ -431,29 +439,39 @@ void cvm::atom_group::parse (std::string const &conf,
cvm::to_str (this->total_mass)+".\n");
cvm::decrease_depth();
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void cvm::atom_group::create_sorted_ids (void)
int cvm::atom_group::create_sorted_ids (void)
{
// Only do the work if the vector is not yet populated
if (sorted_ids.size())
return;
return COLVARS_OK;
std::list<int> temp_id_list;
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
cvm::atom_iter ai;
for (ai = this->begin(); ai != this->end(); ai++) {
temp_id_list.push_back (ai->id);
}
temp_id_list.sort();
temp_id_list.unique();
if (temp_id_list.size() != this->size()) {
cvm::fatal_error ("Error: duplicate atom IDs in atom group? (found " +
cvm::to_str(temp_id_list.size()) +
" unique atom IDs instead of" +
cvm::to_str(this->size()) + ").\n");
cvm::error ("Error: duplicate atom IDs in atom group? (found " +
cvm::to_str(temp_id_list.size()) +
" unique atom IDs instead of" +
cvm::to_str(this->size()) + ").\n");
return COLVARS_ERROR;
}
sorted_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
return;
sorted_ids = std::vector<int> (temp_id_list.size());
unsigned int id_i = 0;
std::list<int>::iterator li;
for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) {
sorted_ids[id_i] = *li;
id_i++;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void cvm::atom_group::center_ref_pos()
@ -464,13 +482,12 @@ void cvm::atom_group::center_ref_pos()
// This is called either by atom_group::parse or by CVCs that set
// reference positions (eg. RMSD, eigenvector)
ref_pos_cog = cvm::atom_pos (0.0, 0.0, 0.0);
std::vector<cvm::atom_pos>::iterator pi = ref_pos.begin();
for ( ; pi != ref_pos.end(); pi++) {
std::vector<cvm::atom_pos>::iterator pi;
for (pi = ref_pos.begin(); pi != ref_pos.end(); ++pi) {
ref_pos_cog += *pi;
}
ref_pos_cog /= (cvm::real) ref_pos.size();
for (std::vector<cvm::atom_pos>::iterator pi = ref_pos.begin();
pi != ref_pos.end(); pi++) {
for (pi = ref_pos.begin(); pi != ref_pos.end(); ++pi) {
(*pi) -= ref_pos_cog;
}
}
@ -679,14 +696,15 @@ void cvm::atom_group::calc_fit_gradients()
std::vector<cvm::atom_pos> cvm::atom_group::positions() const
{
if (b_dummy)
cvm::fatal_error ("Error: positions are not available "
if (b_dummy) {
cvm::error ("Error: positions are not available "
"from a dummy atom group.\n");
}
std::vector<cvm::atom_pos> x (this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator xi = x.begin();
for ( ; ai != this->end(); xi++, ai++) {
for ( ; ai != this->end(); ++xi, ++ai) {
*xi = ai->pos;
}
return x;
@ -694,14 +712,15 @@ std::vector<cvm::atom_pos> cvm::atom_group::positions() const
std::vector<cvm::atom_pos> cvm::atom_group::positions_shifted (cvm::rvector const &shift) const
{
if (b_dummy)
cvm::fatal_error ("Error: positions are not available "
"from a dummy atom group.\n");
if (b_dummy) {
cvm::error ("Error: positions are not available "
"from a dummy atom group.\n");
}
std::vector<cvm::atom_pos> x (this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator xi = x.begin();
for ( ; ai != this->end(); xi++, ai++) {
for ( ; ai != this->end(); ++xi, ++ai) {
*xi = (ai->pos + shift);
}
return x;
@ -709,9 +728,10 @@ std::vector<cvm::atom_pos> cvm::atom_group::positions_shifted (cvm::rvector cons
std::vector<cvm::rvector> cvm::atom_group::velocities() const
{
if (b_dummy)
cvm::fatal_error ("Error: velocities are not available "
"from a dummy atom group.\n");
if (b_dummy) {
cvm::error ("Error: velocities are not available "
"from a dummy atom group.\n");
}
std::vector<cvm::rvector> v (this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
@ -724,14 +744,15 @@ std::vector<cvm::rvector> cvm::atom_group::velocities() const
std::vector<cvm::rvector> cvm::atom_group::system_forces() const
{
if (b_dummy)
cvm::fatal_error ("Error: system forces are not available "
"from a dummy atom group.\n");
if (b_dummy) {
cvm::error ("Error: system forces are not available "
"from a dummy atom group.\n");
}
std::vector<cvm::rvector> f (this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator fi = f.begin();
for ( ; ai != this->end(); fi++, ai++) {
for ( ; ai != this->end(); ++fi, ++ai) {
*fi = ai->system_force;
}
return f;
@ -739,9 +760,10 @@ std::vector<cvm::rvector> cvm::atom_group::system_forces() const
cvm::rvector cvm::atom_group::system_force() const
{
if (b_dummy)
cvm::fatal_error ("Error: system forces are not available "
"from a dummy atom group.\n");
if (b_dummy) {
cvm::error ("Error: system forces are not available "
"from a dummy atom group.\n");
}
cvm::rvector f (0.0);
for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
@ -756,9 +778,11 @@ void cvm::atom_group::apply_colvar_force (cvm::real const &force)
if (b_dummy)
return;
if (noforce)
cvm::fatal_error ("Error: sending a force to a group that has "
"\"enableForces\" set to off.\n");
if (noforce) {
cvm::error ("Error: sending a force to a group that has "
"\"enableForces\" set to off.\n");
return;
}
if (b_rotate) {
@ -803,9 +827,11 @@ void cvm::atom_group::apply_force (cvm::rvector const &force)
if (b_dummy)
return;
if (noforce)
cvm::fatal_error ("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
if (noforce) {
cvm::error ("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
return;
}
if (b_rotate) {
@ -831,12 +857,12 @@ void cvm::atom_group::apply_forces (std::vector<cvm::rvector> const &forces)
return;
if (noforce)
cvm::fatal_error ("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
cvm::error ("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
if (forces.size() != this->size()) {
cvm::fatal_error ("Error: trying to apply an array of forces to an atom "
"group which does not have the same length.\n");
cvm::error ("Error: trying to apply an array of forces to an atom "
"group which does not have the same length.\n");
}
if (b_rotate) {
@ -844,7 +870,7 @@ void cvm::atom_group::apply_forces (std::vector<cvm::rvector> const &forces)
cvm::rotation const rot_inv = rot.inverse();
cvm::atom_iter ai = this->begin();
std::vector<cvm::rvector>::const_iterator fi = forces.begin();
for ( ; ai != this->end(); fi++, ai++) {
for ( ; ai != this->end(); ++fi, ++ai) {
ai->apply_force (rot_inv.rotate (*fi));
}
@ -852,7 +878,7 @@ void cvm::atom_group::apply_forces (std::vector<cvm::rvector> const &forces)
cvm::atom_iter ai = this->begin();
std::vector<cvm::rvector>::const_iterator fi = forces.begin();
for ( ; ai != this->end(); fi++, ai++) {
for ( ; ai != this->end(); ++fi, ++ai) {
ai->apply_force (*fi);
}
}

6
lib/colvars/colvaratoms.h
View File

@ -1,4 +1,4 @@
// -*- c++ -*-
/// -*- c++ -*-
#ifndef COLVARATOMS_H
#define COLVARATOMS_H
@ -137,7 +137,7 @@ public:
std::vector<int> sorted_ids;
/// Allocates and populates the sorted list of atom ids
void create_sorted_ids (void);
int create_sorted_ids (void);
/// \brief When updating atomic coordinates, translate them to align with the
@ -193,7 +193,7 @@ public:
/// \brief Initialize the group by looking up its configuration
/// string in conf and parsing it
void parse (std::string const &conf,
int parse (std::string const &conf,
char const *key);
/// \brief Initialize the group after a temporary vector of atoms

566
lib/colvars/colvarbias.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarbias.h"
@ -27,12 +29,10 @@ colvarbias::colvarbias (std::string const &conf, char const *key)
get_keyval (conf, "name", name, key_str+cvm::to_str (rank));
for (std::vector<colvarbias *>::iterator bi = cvm::biases.begin();
bi != cvm::biases.end();
bi++) {
if ((*bi)->name == this->name)
cvm::fatal_error ("Error: this bias cannot have the same name, \""+this->name+
"\", as another bias.\n");
if (cvm::bias_by_name (this->name) != NULL) {
cvm::error ("Error: this bias cannot have the same name, \""+this->name+
"\", as another bias.\n", INPUT_ERROR);
return;
}
// lookup the associated colvars
@ -43,7 +43,8 @@ colvarbias::colvarbias (std::string const &conf, char const *key)
}
}
if (!colvars.size()) {
cvm::fatal_error ("Error: no collective variables specified.\n");
cvm::error ("Error: no collective variables specified.\n");
return;
}
get_keyval (conf, "outputEnergy", b_output_energy, false);
@ -54,19 +55,45 @@ colvarbias::colvarbias()
: colvarparse(), has_data (false)
{}
colvarbias::~colvarbias()
{
// Remove references to this bias from colvars
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
++cvi) {
for (std::vector<colvarbias *>::iterator bi = (*cvi)->biases.begin();
bi != (*cvi)->biases.end();
++bi) {
if ( *bi == this) {
(*cvi)->biases.erase (bi);
break;
}
}
}
// ...and from the colvars module
for (std::vector<colvarbias *>::iterator bi = cvm::biases.begin();
bi != cvm::biases.end();
++bi) {
if ( *bi == this) {
cvm::biases.erase (bi);
break;
}
}
}
void colvarbias::add_colvar (std::string const &cv_name)
{
if (colvar *cvp = cvm::colvar_p (cv_name)) {
if (colvar *cvp = cvm::colvar_by_name (cv_name)) {
cvp->enable (colvar::task_gradients);
if (cvm::debug())
cvm::log ("Applying this bias to collective variable \""+
cvp->name+"\".\n");
colvars.push_back (cvp);
colvar_forces.push_back (colvarvalue (cvp->type()));
cvp->biases.push_back (this); // add back-reference to this bias to colvar
} else {
cvm::fatal_error ("Error: cannot find a colvar named \""+
cv_name+"\".\n");
cvm::error ("Error: cannot find a colvar named \""+
cv_name+"\".\n");
}
}
@ -86,13 +113,13 @@ void colvarbias::communicate_forces()
void colvarbias::change_configuration(std::string const &conf)
{
cvm::fatal_error ("Error: change_configuration() not implemented.\n");
cvm::error ("Error: change_configuration() not implemented.\n");
}
cvm::real colvarbias::energy_difference(std::string const &conf)
{
cvm::fatal_error ("Error: energy_difference() not implemented.\n");
cvm::error ("Error: energy_difference() not implemented.\n");
return 0.;
}
@ -115,518 +142,3 @@ std::ostream & colvarbias::write_traj (std::ostream &os)
<< bias_energy;
return os;
}
colvarbias_restraint::colvarbias_restraint (std::string const &conf,
char const *key)
: colvarbias (conf, key),
target_nstages (0),
target_nsteps (0)
{
get_keyval (conf, "forceConstant", force_k, 1.0);
// get the initial restraint centers
colvar_centers.resize (colvars.size());
colvar_centers_raw.resize (colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers[i].type (colvars[i]->type());
colvar_centers_raw[i].type (colvars[i]->type());
}
if (get_keyval (conf, "centers", colvar_centers, colvar_centers)) {
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers[i].apply_constraints();
colvar_centers_raw[i] = colvar_centers[i];
}
} else {
colvar_centers.clear();
cvm::fatal_error ("Error: must define the initial centers of the restraints.\n");
}
if (colvar_centers.size() != colvars.size())
cvm::fatal_error ("Error: number of centers does not match "
"that of collective variables.\n");
if (get_keyval (conf, "targetCenters", target_centers, colvar_centers)) {
b_chg_centers = true;
for (size_t i = 0; i < target_centers.size(); i++) {
target_centers[i].apply_constraints();
}
} else {
b_chg_centers = false;
target_centers.clear();
}
if (get_keyval (conf, "targetForceConstant", target_force_k, 0.0)) {
if (b_chg_centers)
cvm::fatal_error ("Error: cannot specify both targetCenters and targetForceConstant.\n");
starting_force_k = force_k;
b_chg_force_k = true;
get_keyval (conf, "targetEquilSteps", target_equil_steps, 0);
get_keyval (conf, "lambdaSchedule", lambda_schedule, lambda_schedule);
if (lambda_schedule.size()) {
// There is one more lambda-point than stages
target_nstages = lambda_schedule.size() - 1;
}
} else {
b_chg_force_k = false;
}
if (b_chg_centers || b_chg_force_k) {
get_keyval (conf, "targetNumSteps", target_nsteps, 0);
if (!target_nsteps)
cvm::fatal_error ("Error: targetNumSteps must be non-zero.\n");
if (get_keyval (conf, "targetNumStages", target_nstages, target_nstages) &&
lambda_schedule.size()) {
cvm::fatal_error ("Error: targetNumStages and lambdaSchedule are incompatible.\n");
}
if (target_nstages) {
// This means that either numStages of lambdaSchedule has been provided
stage = 0;
restraint_FE = 0.0;
}
if (get_keyval (conf, "targetForceExponent", force_k_exp, 1.0)) {
if (! b_chg_force_k)
cvm::log ("Warning: not changing force constant: targetForceExponent will be ignored\n");
if (force_k_exp < 1.0)
cvm::log ("Warning: for all practical purposes, targetForceExponent should be 1.0 or greater.\n");
}
}
get_keyval (conf, "outputCenters", b_output_centers, false);
get_keyval (conf, "outputAccumulatedWork", b_output_acc_work, false);
acc_work = 0.0;
if (cvm::debug())
cvm::log ("Done initializing a new restraint bias.\n");
}
colvarbias_restraint::~colvarbias_restraint ()
{
if (cvm::n_rest_biases > 0)
cvm::n_rest_biases -= 1;
}
void colvarbias_restraint::change_configuration (std::string const &conf)
{
get_keyval (conf, "forceConstant", force_k, force_k);
if (get_keyval (conf, "centers", colvar_centers, colvar_centers)) {
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers[i].apply_constraints();
colvar_centers_raw[i] = colvar_centers[i];
}
}
}
cvm::real colvarbias_restraint::energy_difference (std::string const &conf)
{
std::vector<colvarvalue> alt_colvar_centers;
cvm::real alt_force_k;
cvm::real alt_bias_energy = 0.0;
get_keyval (conf, "forceConstant", alt_force_k, force_k);
alt_colvar_centers.resize (colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
alt_colvar_centers[i].type (colvars[i]->type());
}
if (get_keyval (conf, "centers", alt_colvar_centers, colvar_centers)) {
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers[i].apply_constraints();
}
}
for (size_t i = 0; i < colvars.size(); i++) {
alt_bias_energy += restraint_potential(restraint_convert_k(alt_force_k, colvars[i]->width),
colvars[i],
alt_colvar_centers[i]);
}
return alt_bias_energy - bias_energy;
}
cvm::real colvarbias_restraint::update()
{
bias_energy = 0.0;
if (cvm::debug())
cvm::log ("Updating the restraint bias \""+this->name+"\".\n");
// Setup first stage of staged variable force constant calculation
if (b_chg_force_k && target_nstages && cvm::step_absolute() == 0) {
cvm::real lambda;
if (lambda_schedule.size()) {
lambda = lambda_schedule[0];
} else {
lambda = 0.0;
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow (lambda, force_k_exp);
cvm::log ("Restraint " + this->name + ", stage " +
cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda));
cvm::log ("Setting force constant to " + cvm::to_str (force_k));
}
if (b_chg_centers) {
if (!centers_incr.size()) {
// if this is the first calculation, calculate the advancement
// at each simulation step (or stage, if applicable)
// (take current stage into account: it can be non-zero
// if we are restarting a staged calculation)
centers_incr.resize (colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
centers_incr[i].type (colvars[i]->type());
centers_incr[i] = (target_centers[i] - colvar_centers_raw[i]) /
cvm::real ( target_nstages ? (target_nstages - stage) :
(target_nsteps - cvm::step_absolute()));
}
if (cvm::debug())
cvm::log ("Center increment for the restraint bias \""+
this->name+"\": "+cvm::to_str (centers_incr)+" at stage "+cvm::to_str (stage)+ ".\n");
}
if (target_nstages) {
if ((cvm::step_relative() > 0)
&& (cvm::step_absolute() % target_nsteps) == 0
&& stage < target_nstages) {
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers_raw[i] += centers_incr[i];
colvar_centers[i] = colvar_centers_raw[i];
colvars[i]->wrap(colvar_centers[i]);
colvar_centers[i].apply_constraints();
}
stage++;
cvm::log ("Moving restraint stage " + cvm::to_str(stage) +
" : setting centers to " + cvm::to_str (colvar_centers) +
" at step " + cvm::to_str (cvm::step_absolute()));
}
} else if ((cvm::step_relative() > 0) && (cvm::step_absolute() <= target_nsteps)) {
// move the restraint centers in the direction of the targets
// (slow growth)
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers_raw[i] += centers_incr[i];
colvar_centers[i] = colvar_centers_raw[i];
colvars[i]->wrap(colvar_centers[i]);
colvar_centers[i].apply_constraints();
}
}
if (cvm::debug())
cvm::log ("Current centers for the restraint bias \""+
this->name+"\": "+cvm::to_str (colvar_centers)+".\n");
}
if (b_chg_force_k) {
// Coupling parameter, between 0 and 1
cvm::real lambda;
if (target_nstages) {
// TI calculation: estimate free energy derivative
// need current lambda
if (lambda_schedule.size()) {
lambda = lambda_schedule[stage];
} else {
lambda = cvm::real(stage) / cvm::real(target_nstages);
}
if (target_equil_steps == 0 || cvm::step_absolute() % target_nsteps >= target_equil_steps) {
// Start averaging after equilibration period, if requested
// Square distance normalized by square colvar width
cvm::real dist_sq = 0.0;
for (size_t i = 0; i < colvars.size(); i++) {
dist_sq += colvars[i]->dist2 (colvars[i]->value(), colvar_centers[i])
/ (colvars[i]->width * colvars[i]->width);
}
restraint_FE += 0.5 * force_k_exp * std::pow(lambda, force_k_exp - 1.0)
* (target_force_k - starting_force_k) * dist_sq;
}
// Finish current stage...
if (cvm::step_absolute() % target_nsteps == 0 &&
cvm::step_absolute() > 0) {
cvm::log ("Lambda= " + cvm::to_str (lambda) + " dA/dLambda= "
+ cvm::to_str (restraint_FE / cvm::real(target_nsteps - target_equil_steps)));
// ...and move on to the next one
if (stage < target_nstages) {
restraint_FE = 0.0;
stage++;
if (lambda_schedule.size()) {
lambda = lambda_schedule[stage];
} else {
lambda = cvm::real(stage) / cvm::real(target_nstages);
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow (lambda, force_k_exp);
cvm::log ("Restraint " + this->name + ", stage " +
cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda));
cvm::log ("Setting force constant to " + cvm::to_str (force_k));
}
}
} else if (cvm::step_absolute() <= target_nsteps) {
// update force constant (slow growth)
lambda = cvm::real(cvm::step_absolute()) / cvm::real(target_nsteps);
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow (lambda, force_k_exp);
}
}
if (cvm::debug())
cvm::log ("Done updating the restraint bias \""+this->name+"\".\n");
// Force and energy calculation
for (size_t i = 0; i < colvars.size(); i++) {
colvar_forces[i] = -restraint_force(restraint_convert_k(force_k, colvars[i]->width),
colvars[i],
colvar_centers[i]);
bias_energy += restraint_potential(restraint_convert_k(force_k, colvars[i]->width),
colvars[i],
colvar_centers[i]);
}
if (b_output_acc_work) {
if ((cvm::step_relative() > 0) || (cvm::step_absolute() == 0)) {
for (size_t i = 0; i < colvars.size(); i++) {
// project forces on the calculated increments at this step
acc_work += colvar_forces[i] * centers_incr[i];
}
}
}
if (cvm::debug())
cvm::log ("Current forces for the restraint bias \""+
this->name+"\": "+cvm::to_str (colvar_forces)+".\n");
return bias_energy;
}
std::istream & colvarbias_restraint::read_restart (std::istream &is)
{
size_t const start_pos = is.tellg();
cvm::log ("Restarting restraint bias \""+
this->name+"\".\n");
std::string key, brace, conf;
if ( !(is >> key) || !(key == "restraint" || key == "harmonic") ||
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block ("configuration", conf)) ) {
cvm::log ("Error: in reading restart configuration for restraint bias \""+
this->name+"\" at position "+
cvm::to_str (is.tellg())+" in stream.\n");
is.clear();
is.seekg (start_pos, std::ios::beg);
is.setstate (std::ios::failbit);
return is;
}
// int id = -1;
std::string name = "";
// if ( ( (colvarparse::get_keyval (conf, "id", id, -1, colvarparse::parse_silent)) &&
// (id != this->id) ) ||
if ( (colvarparse::get_keyval (conf, "name", name, std::string (""), colvarparse::parse_silent)) &&
(name != this->name) )
cvm::fatal_error ("Error: in the restart file, the "
"\"restraint\" block has a wrong name\n");
// if ( (id == -1) && (name == "") ) {
if (name.size() == 0) {
cvm::fatal_error ("Error: \"restraint\" block in the restart file "
"has no identifiers.\n");
}
if (b_chg_centers) {
// cvm::log ("Reading the updated restraint centers from the restart.\n");
if (!get_keyval (conf, "centers", colvar_centers))
cvm::fatal_error ("Error: restraint centers are missing from the restart.\n");
if (!get_keyval (conf, "centers_raw", colvar_centers_raw))
cvm::fatal_error ("Error: \"raw\" restraint centers are missing from the restart.\n");
}
if (b_chg_force_k) {
// cvm::log ("Reading the updated force constant from the restart.\n");
if (!get_keyval (conf, "forceConstant", force_k))
cvm::fatal_error ("Error: force constant is missing from the restart.\n");
}
if (target_nstages) {
// cvm::log ("Reading current stage from the restart.\n");
if (!get_keyval (conf, "stage", stage))
cvm::fatal_error ("Error: current stage is missing from the restart.\n");
}
if (b_output_acc_work) {
if (!get_keyval (conf, "accumulatedWork", acc_work))
cvm::fatal_error ("Error: accumulatedWork is missing from the restart.\n");
}
is >> brace;
if (brace != "}") {
cvm::fatal_error ("Error: corrupt restart information for restraint bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str (is.tellg())+" in the restart file.\n");
is.setstate (std::ios::failbit);
}
return is;
}
std::ostream & colvarbias_restraint::write_restart (std::ostream &os)
{
os << "restraint {\n"
<< " configuration {\n"
// << " id " << this->id << "\n"
<< " name " << this->name << "\n";
if (b_chg_centers) {
os << " centers ";
for (size_t i = 0; i < colvars.size(); i++) {
os << " " << colvar_centers[i];
}
os << "\n";
os << " centers_raw ";
for (size_t i = 0; i < colvars.size(); i++) {
os << " " << colvar_centers_raw[i];
}
os << "\n";
}
if (b_chg_force_k) {
os << " forceConstant "
<< std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << force_k << "\n";
}
if (target_nstages) {
os << " stage " << std::setw (cvm::it_width)
<< stage << "\n";
}
if (b_output_acc_work) {
os << " accumulatedWork " << acc_work << "\n";
}
os << " }\n"
<< "}\n\n";
return os;
}
std::ostream & colvarbias_restraint::write_traj_label (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " E_"
<< cvm::wrap_string (this->name, cvm::en_width-2);
if (b_output_centers)
for (size_t i = 0; i < colvars.size(); i++) {
size_t const this_cv_width = (colvars[i]->value()).output_width (cvm::cv_width);
os << " x0_"
<< cvm::wrap_string (colvars[i]->name, this_cv_width-3);
}
if (b_output_acc_work)
os << " W_"
<< cvm::wrap_string (this->name, cvm::en_width-2);
return os;
}
std::ostream & colvarbias_restraint::write_traj (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " "
<< std::setprecision (cvm::en_prec) << std::setw (cvm::en_width)
<< bias_energy;
if (b_output_centers)
for (size_t i = 0; i < colvars.size(); i++) {
os << " "
<< std::setprecision (cvm::cv_prec) << std::setw (cvm::cv_width)
<< colvar_centers[i];
}
if (b_output_acc_work)
os << " "
<< std::setprecision (cvm::en_prec) << std::setw (cvm::en_width)
<< acc_work;
return os;
}
colvarbias_restraint_harmonic::colvarbias_restraint_harmonic(std::string const &conf, char const *key) :
colvarbias_restraint(conf, key) {
for (size_t i = 0; i < colvars.size(); i++) {
if (colvars[i]->width != 1.0)
cvm::log ("The force constant for colvar \""+colvars[i]->name+
"\" will be rescaled to "+
cvm::to_str (restraint_convert_k(force_k, colvars[i]->width))+
" according to the specified width.\n");
}
}
cvm::real colvarbias_restraint_harmonic::restraint_potential(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return 0.5 * k * x->dist2(x->value(), xcenter);
}
colvarvalue colvarbias_restraint_harmonic::restraint_force(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return 0.5 * k * x->dist2_lgrad(x->value(), xcenter);
}
cvm::real colvarbias_restraint_harmonic::restraint_convert_k(cvm::real k, cvm::real dist_measure) const
{
return k / (dist_measure * dist_measure);
}
colvarbias_restraint_linear::colvarbias_restraint_linear(std::string const &conf, char const *key) :
colvarbias_restraint(conf, key) {
for (size_t i = 0; i < colvars.size(); i++) {
if (colvars[i]->width != 1.0)
cvm::log ("The force constant for colvar \""+colvars[i]->name+
"\" will be rescaled to "+
cvm::to_str (restraint_convert_k(force_k, colvars[i]->width))+
" according to the specified width.\n");
}
}
cvm::real colvarbias_restraint_linear::restraint_potential(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return k * (x->value() - xcenter);
}
colvarvalue colvarbias_restraint_linear::restraint_force(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return k;
}
cvm::real colvarbias_restraint_linear::restraint_convert_k(cvm::real k, cvm::real dist_measure) const
{
return k / dist_measure;
}

166
lib/colvars/colvarbias.h
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#ifndef COLVARBIAS_H
#define COLVARBIAS_H
@ -9,9 +11,6 @@
class colvarbias : public colvarparse {
public:
/// Numeric id of this bias
int id;
/// Name of this bias
std::string name;
@ -22,6 +21,8 @@ public:
/// Return bias energy
virtual cvm::real update() = 0;
// TODO: move update_bias here (share with metadynamics)
/// Load new configuration - force constant and/or centers only
virtual void change_configuration(std::string const &conf);
@ -44,7 +45,7 @@ public:
colvarbias();
/// Destructor
virtual inline ~colvarbias() {}
virtual ~colvarbias();
/// Read the bias configuration from a restart file
virtual std::istream & read_restart (std::istream &is) = 0;
@ -58,7 +59,9 @@ public:
/// Output quantities such as the bias energy to the trajectory file
virtual std::ostream & write_traj (std::ostream &os);
inline cvm::real get_energy () {
return bias_energy;
}
protected:
/// \brief Pointers to collective variables to which the bias is
@ -81,157 +84,4 @@ protected:
};
/// \brief Bias restraint, optionally moving towards a target
/// (implementation of \link colvarbias \endlink)
class colvarbias_restraint : public colvarbias {
public:
/// Retrieve colvar values and calculate their biasing forces
virtual cvm::real update();
/// Load new configuration - force constant and/or centers only
virtual void change_configuration(std::string const &conf);
/// Calculate change in energy from using alternate configuration
virtual cvm::real energy_difference(std::string const &conf);
/// Read the bias configuration from a restart file
virtual std::istream & read_restart (std::istream &is);
/// Write the bias configuration to a restart file
virtual std::ostream & write_restart (std::ostream &os);
/// Write a label to the trajectory file (comment line)
virtual std::ostream & write_traj_label (std::ostream &os);
/// Output quantities such as the bias energy to the trajectory file
virtual std::ostream & write_traj (std::ostream &os);
/// \brief Constructor
colvarbias_restraint (std::string const &conf, char const *key);
/// Destructor
virtual ~colvarbias_restraint();
protected:
/// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const = 0;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const = 0;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const = 0;
/// \brief Restraint centers
std::vector<colvarvalue> colvar_centers;
/// \brief Restraint centers without wrapping or constraints applied
std::vector<colvarvalue> colvar_centers_raw;
/// \brief Moving target?
bool b_chg_centers;
/// \brief New restraint centers
std::vector<colvarvalue> target_centers;
/// \brief Amplitude of the restraint centers' increment at each step
/// (or stage) towards the new values (calculated from target_nsteps)
std::vector<colvarvalue> centers_incr;
/// Whether to write the current restraint centers to the trajectory file
bool b_output_centers;
/// Whether to write the current accumulated work to the trajectory file
bool b_output_acc_work;
/// \brief Accumulated work
cvm::real acc_work;
/// \brief Restraint force constant
cvm::real force_k;
/// \brief Changing force constant?
bool b_chg_force_k;
/// \brief Restraint force constant (target value)
cvm::real target_force_k;
/// \brief Restraint force constant (starting value)
cvm::real starting_force_k;
/// \brief Lambda-schedule for custom varying force constant
std::vector<cvm::real> lambda_schedule;
/// \brief Exponent for varying the force constant
cvm::real force_k_exp;
/// \brief Intermediate quantity to compute the restraint free energy
/// (in TI, would be the accumulating FE derivative)
cvm::real restraint_FE;
/// \brief Equilibration steps for restraint FE calculation through TI
cvm::real target_equil_steps;
/// \brief Number of stages over which to perform the change
/// If zero, perform a continuous change
int target_nstages;
/// \brief Number of current stage of the perturbation
int stage;
/// \brief Number of steps required to reach the target force constant
/// or restraint centers
size_t target_nsteps;
};
/// \brief Harmonic bias restraint
/// (implementation of \link colvarbias_restraint \endlink)
class colvarbias_restraint_harmonic : public colvarbias_restraint {
public:
colvarbias_restraint_harmonic(std::string const &conf, char const *key);
protected: /// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
};
/// \brief Linear bias restraint
/// (implementation of \link colvarbias_restraint \endlink)
class colvarbias_restraint_linear : public colvarbias_restraint {
public:
colvarbias_restraint_linear(std::string const &conf, char const *key);
protected: /// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
};
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

60
lib/colvars/colvarbias_abf.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
/********************************************************************************
* Implementation of the ABF and histogram biases *
********************************************************************************/
@ -13,6 +15,7 @@ colvarbias_abf::colvarbias_abf (std::string const &conf, char const *key)
gradients (NULL),
samples (NULL)
{
// TODO relax this in case of VMD plugin
if (cvm::temperature() == 0.0)
cvm::log ("WARNING: ABF should not be run without a thermostat or at 0 Kelvin!\n");
@ -44,13 +47,13 @@ colvarbias_abf::colvarbias_abf (std::string const &conf, char const *key)
// ************* checking the associated colvars *******************
if (colvars.size() == 0) {
cvm::fatal_error ("Error: no collective variables specified for the ABF bias.\n");
cvm::error ("Error: no collective variables specified for the ABF bias.\n");
}
for (size_t i = 0; i < colvars.size(); i++) {
if (colvars[i]->type() != colvarvalue::type_scalar) {
cvm::fatal_error ("Error: ABF bias can only use scalar-type variables.\n");
cvm::error ("Error: ABF bias can only use scalar-type variables.\n");
}
colvars[i]->enable (colvar::task_gradients);
@ -84,11 +87,11 @@ colvarbias_abf::colvarbias_abf (std::string const &conf, char const *key)
if (get_keyval (conf, "maxForce", max_force)) {
if (max_force.size() != colvars.size()) {
cvm::fatal_error ("Error: Number of parameters to maxForce does not match number of colvars.");
cvm::error ("Error: Number of parameters to maxForce does not match number of colvars.");
}
for (size_t i=0; i<colvars.size(); i++) {
if (max_force[i] < 0.0) {
cvm::fatal_error ("Error: maxForce should be non-negative.");
cvm::error ("Error: maxForce should be non-negative.");
}
}
cap_force = true;
@ -241,13 +244,13 @@ void colvarbias_abf::write_gradients_samples (const std::string &prefix, bool ap
if (!append) cvm::backup_file (samples_out_name.c_str());
samples_os.open (samples_out_name.c_str(), mode);
if (!samples_os.good()) cvm::fatal_error ("Error opening ABF samples file " + samples_out_name + " for writing");
if (!samples_os.good()) cvm::error ("Error opening ABF samples file " + samples_out_name + " for writing");
samples->write_multicol (samples_os);
samples_os.close ();
if (!append) cvm::backup_file (gradients_out_name.c_str());
gradients_os.open (gradients_out_name.c_str(), mode);
if (!gradients_os.good()) cvm::fatal_error ("Error opening ABF gradient file " + gradients_out_name + " for writing");
if (!gradients_os.good()) cvm::error ("Error opening ABF gradient file " + gradients_out_name + " for writing");
gradients->write_multicol (gradients_os);
gradients_os.close ();
@ -257,7 +260,7 @@ void colvarbias_abf::write_gradients_samples (const std::string &prefix, bool ap
std::ofstream pmf_os;
// Do numerical integration and output a PMF
pmf_os.open (pmf_out_name.c_str(), mode);
if (!pmf_os.good()) cvm::fatal_error ("Error opening pmf file " + pmf_out_name + " for writing");
if (!pmf_os.good()) cvm::error ("Error opening pmf file " + pmf_out_name + " for writing");
gradients->write_1D_integral (pmf_os);
pmf_os << std::endl;
pmf_os.close ();
@ -278,13 +281,13 @@ void colvarbias_abf::read_gradients_samples ()
cvm::log ("Reading sample count from " + samples_in_name + " and gradients from " + gradients_in_name);
is.open (samples_in_name.c_str());
if (!is.good()) cvm::fatal_error ("Error opening ABF samples file " + samples_in_name + " for reading");
if (!is.good()) cvm::error ("Error opening ABF samples file " + samples_in_name + " for reading");
samples->read_multicol (is, true);
is.close ();
is.clear();
is.open (gradients_in_name.c_str());
if (!is.good()) cvm::fatal_error ("Error opening ABF gradient file " + gradients_in_name + " for reading");
if (!is.good()) cvm::error ("Error opening ABF gradient file " + gradients_in_name + " for reading");
gradients->read_multicol (is, true);
is.close ();
}
@ -319,7 +322,7 @@ std::ostream & colvarbias_abf::write_restart (std::ostream& os)
std::istream & colvarbias_abf::read_restart (std::istream& is)
{
if ( input_prefix.size() > 0 ) {
cvm::fatal_error ("ERROR: cannot provide both inputPrefix and restart information (colvarsInput)");
cvm::error ("ERROR: cannot provide both inputPrefix and restart information (colvarsInput)");
}
size_t const start_pos = is.tellg();
@ -343,10 +346,10 @@ std::istream & colvarbias_abf::read_restart (std::istream& is)
std::string name = "";
if ( (colvarparse::get_keyval (conf, "name", name, std::string (""), colvarparse::parse_silent)) &&
(name != this->name) )
cvm::fatal_error ("Error: in the restart file, the "
cvm::error ("Error: in the restart file, the "
"\"abf\" block has wrong name (" + name + ")\n");
if ( name == "" ) {
cvm::fatal_error ("Error: \"abf\" block in the restart file has no name.\n");
cvm::error ("Error: \"abf\" block in the restart file has no name.\n");
}
if ( !(is >> key) || !(key == "samples")) {
@ -359,7 +362,10 @@ std::istream & colvarbias_abf::read_restart (std::istream& is)
return is;
}
if (! samples->read_raw (is)) {
samples->read_raw_error();
is.clear();
is.seekg (start_pos, std::ios::beg);
is.setstate (std::ios::failbit);
return is;
}
if ( !(is >> key) || !(key == "gradient")) {
@ -372,12 +378,15 @@ std::istream & colvarbias_abf::read_restart (std::istream& is)
return is;
}
if (! gradients->read_raw (is)) {
gradients->read_raw_error();
is.clear();
is.seekg (start_pos, std::ios::beg);
is.setstate (std::ios::failbit);
return is;
}
is >> brace;
if (brace != "}") {
cvm::fatal_error ("Error: corrupt restart information for ABF bias \""+
cvm::error ("Error: corrupt restart information for ABF bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str (is.tellg())+" in the restart file.\n");
is.setstate (std::ios::failbit);
@ -397,7 +406,7 @@ colvarbias_histogram::colvarbias_histogram (std::string const &conf, char const
get_keyval (conf, "outputfreq", output_freq, cvm::restart_out_freq);
if ( output_freq == 0 ) {
cvm::fatal_error ("User required histogram with zero output frequency");
cvm::error ("User required histogram with zero output frequency");
}
grid = new colvar_grid_count (colvars);
@ -440,7 +449,7 @@ cvm::real colvarbias_histogram::update()
if (cvm::debug()) cvm::log ("Histogram bias trying to write grid to disk");
grid_os.open (out_name.c_str());
if (!grid_os.good()) cvm::fatal_error ("Error opening histogram file " + out_name + " for writing");
if (!grid_os.good()) cvm::error ("Error opening histogram file " + out_name + " for writing");
grid->write_multicol (grid_os);
grid_os.close ();
}
@ -472,15 +481,15 @@ std::istream & colvarbias_histogram::read_restart (std::istream& is)
std::string name = "";
if ( (colvarparse::get_keyval (conf, "name", name, std::string (""), colvarparse::parse_silent)) &&
(name != this->name) )
cvm::fatal_error ("Error: in the restart file, the "
cvm::error ("Error: in the restart file, the "
"\"histogram\" block has a wrong name: different system?\n");
if ( (id == -1) && (name == "") ) {
cvm::fatal_error ("Error: \"histogram\" block in the restart file "
cvm::error ("Error: \"histogram\" block in the restart file "
"has no name.\n");
}
if ( !(is >> key) || !(key == "grid")) {
cvm::log ("Error: in reading restart configuration for histogram \""+
cvm::error ("Error: in reading restart configuration for histogram \""+
this->name+"\" at position "+
cvm::to_str (is.tellg())+" in stream.\n");
is.clear();
@ -489,14 +498,17 @@ std::istream & colvarbias_histogram::read_restart (std::istream& is)
return is;
}
if (! grid->read_raw (is)) {
grid->read_raw_error();
is.clear();
is.seekg (start_pos, std::ios::beg);
is.setstate (std::ios::failbit);
return is;
}
is >> brace;
if (brace != "}") {
cvm::fatal_error ("Error: corrupt restart information for ABF bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str (is.tellg())+" in the restart file.\n");
cvm::error ("Error: corrupt restart information for ABF bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str (is.tellg())+" in the restart file.\n");
is.setstate (std::ios::failbit);
}
return is;

2
lib/colvars/colvarbias_abf.h
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
/************************************************************************
* Headers for the ABF and histogram biases *
************************************************************************/

42
lib/colvars/colvarbias_alb.cpp
View File

@ -13,6 +13,7 @@
colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
colvarbias(conf, key), update_calls(0), b_equilibration(true) {
size_t i;
// get the initial restraint centers
colvar_centers.resize (colvars.size());
@ -29,7 +30,7 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
coupling_rate.resize(colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
for (i = 0; i < colvars.size(); i++) {
colvar_centers[i].type (colvars[i]->type());
//zero moments
means[i] = ssd[i] = 0;
@ -39,7 +40,7 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
}
if (get_keyval (conf, "centers", colvar_centers, colvar_centers)) {
for (size_t i = 0; i < colvars.size(); i++) {
for (i = 0; i < colvars.size(); i++) {
colvar_centers[i].apply_constraints();
}
} else {
@ -52,7 +53,7 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
"that of collective variables.\n");
if(!get_keyval (conf, "UpdateFrequency", update_freq, 0))
cvm::fatal_error("Error: must set updateFrequency for apadtive linear bias.\n");
cvm::fatal_error("Error: must set updateFrequency for adaptive linear bias.\n");
//we split the time between updating and equilibrating
update_freq /= 2;
@ -67,21 +68,21 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
//initial guess
if(!get_keyval (conf, "forceConstant", set_coupling, set_coupling))
for(size_t i =0 ; i < colvars.size(); i++)
for(i =0 ; i < colvars.size(); i++)
set_coupling[i] = 0.;
//how we're going to increase to that point
for(size_t i = 0; i < colvars.size(); i++)
for(i = 0; i < colvars.size(); i++)
coupling_rate[i] = (set_coupling[i] - current_coupling[i]) / update_freq;
if(!get_keyval (conf, "forceRange", max_coupling_range, max_coupling_range)) {
//set to default
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
if(cvm::temperature() > 0)
max_coupling_range[i] = 3 * cvm::temperature() * cvm::boltzmann();
max_coupling_range[i] = 3 * cvm::temperature() * cvm::boltzmann();
else
max_coupling_range[i] = 3 * cvm::boltzmann();
max_coupling_range[i] = 3 * cvm::boltzmann();
}
}
@ -89,7 +90,7 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
if(!get_keyval (conf, "rateMax", max_coupling_rate, max_coupling_rate)) {
//set to default
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
max_coupling_rate[i] = max_coupling_range[i] / (10 * update_freq);
}
}
@ -123,9 +124,9 @@ cvm::real colvarbias_alb::update() {
bool finished_equil_flag = 1;
cvm::real delta;
for (size_t i = 0; i < colvars.size(); i++) {
colvar_forces[i] = -restraint_force(restraint_convert_k(current_coupling[i], colvars[i]->width),
colvars[i],
colvar_centers[i]);
colvar_forces[i] = -1.0 * restraint_force(restraint_convert_k(current_coupling[i], colvars[i]->width),
colvars[i],
colvar_centers[i]);
bias_energy += restraint_potential(restraint_convert_k(current_coupling[i], colvars[i]->width),
colvars[i],
colvar_centers[i]);
@ -193,7 +194,7 @@ cvm::real colvarbias_alb::update() {
ssd[i] = 0;
//stochastic if we do that update or not
if(colvars.size() == 1 || rand() < RAND_MAX / colvars.size()) {
if(colvars.size() == 1 || rand() < RAND_MAX / ((int) colvars.size())) {
coupling_accum[i] += step_size * step_size;
current_coupling[i] = set_coupling[i];
set_coupling[i] += max_coupling_range[i] / sqrt(coupling_accum[i]) * step_size;
@ -294,37 +295,38 @@ std::ostream & colvarbias_alb::write_restart (std::ostream &os)
<< " configuration {\n"
<< " name " << this->name << "\n";
os << " setCoupling ";
for(size_t i = 0; i < colvars.size(); i++) {
size_t i;
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << set_coupling[i] << "\n";
}
os << " currentCoupling ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << current_coupling[i] << "\n";
}
os << " maxCouplingRange ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << max_coupling_range[i] << "\n";
}
os << " couplingRate ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << coupling_rate[i] << "\n";
}
os << " couplingAccum ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << coupling_accum[i] << "\n";
}
os << " mean ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << means[i] << "\n";
}
os << " ssd ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << ssd[i] << "\n";
}

2
lib/colvars/colvarbias_alb.h
View File

@ -2,7 +2,7 @@
#define COLVARBIAS_ALB_H
#include "colvar.h"
#include "colvarbias.h"
#include "colvarbias_restraint.h"
class colvarbias_alb : public colvarbias {

77
lib/colvars/colvarbias_meta.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include <iostream>
#include <sstream>
#include <fstream>
@ -64,7 +66,8 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
get_keyval (conf, "rebinGrids", rebin_grids, false);
expand_grids = false;
for (size_t i = 0; i < colvars.size(); i++) {
size_t i;
for (i = 0; i < colvars.size(); i++) {
if (colvars[i]->expand_boundaries) {
expand_grids = true;
cvm::log ("Metadynamics bias \""+this->name+"\""+
@ -79,7 +82,7 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
get_keyval (conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent);
get_keyval (conf, "saveFreeEnergyFile", dump_fes_save, false);
for (size_t i = 0; i < colvars.size(); i++) {
for (i = 0; i < colvars.size(); i++) {
colvars[i]->enable (colvar::task_grid);
}
@ -91,6 +94,9 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
dump_fes = false;
dump_fes_save = false;
dump_replica_fes = false;
hills_energy = NULL;
hills_energy_gradients = NULL;
}
if (comm != single_replica) {
@ -144,7 +150,7 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
replica_state_file =
(std::string (pwd)+std::string (PATHSEP)+
cvm::output_prefix+".colvars."+this->name+"."+replica_id+".state");
delete pwd;
delete[] pwd;
}
// now register this replica
@ -316,7 +322,7 @@ colvarbias_meta::delete_hill (hill_iter &h)
"")+".\n");
}
if (use_grids && hills_off_grid.size()) {
if (use_grids && !hills_off_grid.empty()) {
for (hill_iter hoff = hills_off_grid.begin();
hoff != hills_off_grid.end(); hoff++) {
if (*h == *hoff) {
@ -458,9 +464,14 @@ cvm::real colvarbias_meta::update()
case single_replica:
if (well_tempered) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
cvm::real const hills_energy_sum_here = hills_energy->value(curr_bin);
cvm::real const exp_weight = std::exp(-hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
cvm::real hills_energy_sum_here = 0.0;
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
hills_energy_sum_here = hills_energy->value(curr_bin);
} else {
calc_hills (new_hills_begin, hills.end(), hills_energy_sum_here);
}
cvm::real const exp_weight = std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
create_hill (hill ((hill_weight*exp_weight), colvars, hill_width));
} else {
create_hill (hill (hill_weight, colvars, hill_width));
@ -469,9 +480,14 @@ cvm::real colvarbias_meta::update()
case multiple_replicas:
if (well_tempered) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
cvm::real const hills_energy_sum_here = hills_energy->value(curr_bin);
cvm::real const exp_weight = std::exp(-hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
cvm::real hills_energy_sum_here = 0.0;
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
hills_energy_sum_here = hills_energy->value(curr_bin);
} else {
calc_hills (new_hills_begin, hills.end(), hills_energy_sum_here);
}
cvm::real const exp_weight = std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
create_hill (hill ((hill_weight*exp_weight), colvars, hill_width, replica_id));
} else {
create_hill (hill (hill_weight, colvars, hill_width, replica_id));
@ -680,10 +696,11 @@ void colvarbias_meta::calc_hills_force (size_t const &i,
// were already saved with their types matching those in the
// colvars)
hill_iter h;
switch (colvars[i]->type()) {
case colvarvalue::type_scalar:
for (hill_iter h = h_first; h != h_last; h++) {
for (h = h_first; h != h_last; h++) {
if (h->value() == 0.0) continue;
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
@ -695,7 +712,8 @@ void colvarbias_meta::calc_hills_force (size_t const &i,
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
for (hill_iter h = h_first; h != h_last; h++) {
case colvarvalue::type_unitvectorderiv:
for (h = h_first; h != h_last; h++) {
if (h->value() == 0.0) continue;
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
@ -705,8 +723,8 @@ void colvarbias_meta::calc_hills_force (size_t const &i,
}
break;
case colvarvalue::type_quaternion:
for (hill_iter h = h_first; h != h_last; h++) {
case colvarvalue::type_quaternionderiv:
for (h = h_first; h != h_last; h++) {
if (h->value() == 0.0) continue;
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
@ -717,6 +735,7 @@ void colvarbias_meta::calc_hills_force (size_t const &i,
break;
case colvarvalue::type_notset:
case colvarvalue::type_all:
break;
}
}
@ -756,8 +775,8 @@ void colvarbias_meta::project_hills (colvarbias_meta::hill_iter h_first,
for ( ;
(he->index_ok (he_ix)) && (hg->index_ok (hg_ix));
count++) {
for (size_t i = 0; i < colvars.size(); i++) {
size_t i;
for (i = 0; i < colvars.size(); i++) {
colvar_values[i] = hills_energy->bin_to_value_scalar (he_ix[i], i);
}
@ -766,7 +785,7 @@ void colvarbias_meta::project_hills (colvarbias_meta::hill_iter h_first,
calc_hills (h_first, h_last, hills_energy_here, colvar_values);
he->acc_value (he_ix, hills_energy_here);
for (size_t i = 0; i < colvars.size(); i++) {
for (i = 0; i < colvars.size(); i++) {
hills_forces_here[i].reset();
calc_hills_force (i, h_first, h_last, hills_forces_here, colvar_values);
colvar_forces_scalar[i] = hills_forces_here[i].real_value;
@ -935,10 +954,6 @@ void colvarbias_meta::update_replicas_registry()
}
}
}
// continue the cycle
new_replica_file = "";
new_replica = "";
} else {
cvm::fatal_error ("Error: cannot read the replicas registry file \""+
replicas_registry+"\".\n");
@ -1279,7 +1294,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
}
}
bool const existing_hills = (hills.size() > 0);
bool const existing_hills = !hills.empty();
size_t const old_hills_size = hills.size();
hill_iter old_hills_end = hills.end();
hill_iter old_hills_off_grid_end = hills_off_grid.end();
@ -1299,7 +1314,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
cvm::log ("Read "+cvm::to_str (hills.size())+
" hills in addition to the grids.\n");
} else {
if (hills.size())
if (!hills.empty())
cvm::log ("Read "+cvm::to_str (hills.size())+" hills.\n");
}
@ -1314,7 +1329,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
colvar_grid_gradient *new_hills_energy_gradients =
new colvar_grid_gradient (colvars);
if (!grids_from_restart_file || (keep_hills && hills.size())) {
if (!grids_from_restart_file || (keep_hills && !hills.empty())) {
// if there are hills, recompute the new grids from them
cvm::log ("Rebinning the energy and forces grids from "+
cvm::to_str (hills.size())+" hills (this may take a while)...\n");
@ -1337,12 +1352,12 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
// assuming that some boundaries have expanded, eliminate those
// off-grid hills that aren't necessary any more
if (hills.size())
if (!hills.empty())
recount_hills_off_grid (hills.begin(), hills.end(), hills_energy);
}
if (use_grids) {
if (hills_off_grid.size()) {
if (!hills_off_grid.empty()) {
cvm::log (cvm::to_str (hills_off_grid.size())+" hills are near the "
"grid boundaries: they will be computed analytically "
"and saved to the state files.\n");
@ -1656,15 +1671,16 @@ std::string colvarbias_meta::hill::output_traj()
os.setf (std::ios::scientific, std::ios::floatfield);
size_t i;
os << " ";
for (size_t i = 0; i < centers.size(); i++) {
for (i = 0; i < centers.size(); i++) {
os << " ";
os << std::setprecision (cvm::cv_prec)
<< std::setw (cvm::cv_width) << centers[i];
}
os << " ";
for (size_t i = 0; i < widths.size(); i++) {
for (i = 0; i < widths.size(); i++) {
os << " ";
os << std::setprecision (cvm::cv_prec)
<< std::setw (cvm::cv_width) << widths[i];
@ -1692,8 +1708,9 @@ std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
if (h.replica.size())
os << " replicaID " << h.replica << "\n";
size_t i;
os << " centers ";
for (size_t i = 0; i < (h.centers).size(); i++) {
for (i = 0; i < (h.centers).size(); i++) {
os << " "
<< std::setprecision (cvm::cv_prec)
<< std::setw (cvm::cv_width)
@ -1702,7 +1719,7 @@ std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
os << "\n";
os << " widths ";
for (size_t i = 0; i < (h.widths).size(); i++) {
for (i = 0; i < (h.widths).size(); i++) {
os << " "
<< std::setprecision (cvm::cv_prec)
<< std::setw (cvm::cv_width)

10
lib/colvars/colvarbias_meta.h
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#ifndef COLVARBIAS_META_H
#define COLVARBIAS_META_H
@ -224,7 +226,7 @@ protected:
std::ofstream replica_hills_os;
/// Position within replica_hills_file (when reading it)
size_t replica_hills_file_pos;
int replica_hills_file_pos;
};
@ -417,9 +419,3 @@ public:
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

53
lib/colvars/colvarcomp.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvar.h"
@ -78,18 +80,14 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
// this function should work for any scalar variable:
// the only difference will be the name of the atom group (here, "group")
// collect into a vector for convenience
std::vector<cvm::rvector> gradients (group.size());
for (size_t i = 0; i < group.size(); i++) {
gradients[i] = group[i].grad;
}
if (group.b_dummy) return;
cvm::rotation const rot_0 = group.rot;
cvm::rotation const rot_inv = group.rot.inverse();
cvm::real const x_0 = x.real_value;
cvm::log ("gradients = "+cvm::to_str (gradients)+"\n");
// cvm::log ("gradients = "+cvm::to_str (gradients)+"\n");
// it only makes sense to debug the fit gradients
// when the fitting group is the same as this group
@ -131,7 +129,8 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
cvm::log ("Atom "+cvm::to_str (ia)+", component "+cvm::to_str (id)+":\n");
cvm::log ("dx(actual) = "+cvm::to_str (x_1 - x_0,
21, 14)+"\n");
cvm::real const dx_pred = (group.fit_gradients.size() && (group.ref_pos_group == NULL)) ?
//cvm::real const dx_pred = (group.fit_gradients.size() && (group.ref_pos_group == NULL)) ?
cvm::real const dx_pred = (group.fit_gradients.size()) ?
(cvm::debug_gradients_step_size * (atom_grad[id] + group.fit_gradients[ia][id])) :
(cvm::debug_gradients_step_size * atom_grad[id]);
cvm::log ("dx(interp) = "+cvm::to_str (dx_pred,
@ -141,7 +140,45 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
std::fabs (x_1 - x_0),
12, 5)+
".\n");
}
}
/*
* The code below is WIP
*/
// if (group.ref_pos_group != NULL) {
// cvm::atom_group &ref = *group.ref_pos_group;
// group.calc_fit_gradients();
//
// for (size_t ia = 0; ia < ref.size(); ia++) {
//
// for (size_t id = 0; id < 3; id++) {
// // (re)read original positions
// group.read_positions();
// ref.read_positions();
// // change one coordinate
// ref[ia].pos[id] += cvm::debug_gradients_step_size;
// group.calc_apply_roto_translation();
// calc_value();
// cvm::real const x_1 = x.real_value;
// cvm::log ("refPosGroup atom "+cvm::to_str (ia)+", component "+cvm::to_str (id)+":\n");
// cvm::log ("dx(actual) = "+cvm::to_str (x_1 - x_0,
// 21, 14)+"\n");
// //cvm::real const dx_pred = (group.fit_gradients.size() && (group.ref_pos_group == NULL)) ?
// // cvm::real const dx_pred = (group.fit_gradients.size()) ?
// // (cvm::debug_gradients_step_size * (atom_grad[id] + group.fit_gradients[ia][id])) :
// // (cvm::debug_gradients_step_size * atom_grad[id]);
// cvm::real const dx_pred = cvm::debug_gradients_step_size * ref.fit_gradients[ia][id];
// cvm::log ("dx(interp) = "+cvm::to_str (dx_pred,
// 21, 14)+"\n");
// cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
// cvm::to_str (std::fabs (x_1 - x_0 - dx_pred) /
// std::fabs (x_1 - x_0),
// 12, 5)+
// ".\n");
// }
// }
// }
return;
}

52
lib/colvars/colvarcomp.h
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#ifndef COLVARCOMP_H
#define COLVARCOMP_H
@ -153,6 +155,9 @@ public:
/// \brief Return the previously calculated value
virtual colvarvalue value() const;
/// \brief Return const pointer to the previously calculated value
virtual const colvarvalue *p_value() const;
/// \brief Return the previously calculated system force
virtual colvarvalue system_force() const;
@ -261,6 +266,11 @@ inline colvarvalue colvar::cvc::value() const
return x;
}
inline const colvarvalue * colvar::cvc::p_value() const
{
return &x;
}
inline colvarvalue colvar::cvc::system_force() const
{
return ft;
@ -296,8 +306,8 @@ inline cvm::real colvar::cvc::compare (colvarvalue const &x1,
if (this->type() == colvarvalue::type_scalar) {
return cvm::real (x1 - x2);
} else {
cvm::fatal_error ("Error: you requested an operation which requires "
"comparison between two non-scalar values.\n");
cvm::error ("Error: you requested an operation which requires "
"comparison between two non-scalar values.\n");
return 0.0;
}
}
@ -1050,6 +1060,31 @@ public:
};
/// \brief Colvar component: cosine of the angle of rotation with respect to a set
/// of reference coordinates (colvarvalue::type_scalar type, range
/// [-1:1])
class colvar::orientation_proj
: public colvar::orientation
{
public:
orientation_proj (std::string const &conf);
orientation_proj();
virtual inline ~orientation_proj() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force (colvarvalue const &force);
virtual cvm::real dist2 (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual cvm::real compare (colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: projection of the orientation vector onto
/// a predefined axis (colvarvalue::type_scalar type, range [-1:1])
class colvar::tilt
@ -1199,6 +1234,7 @@ public:
simple_scalar_dist_functions (inertia_z)
simple_scalar_dist_functions (rmsd)
simple_scalar_dist_functions (orientation_angle)
simple_scalar_dist_functions (orientation_proj)
simple_scalar_dist_functions (tilt)
simple_scalar_dist_functions (eigenvector)
// simple_scalar_dist_functions (alpha_dihedrals)
@ -1379,7 +1415,7 @@ inline colvarvalue colvar::distance_vec::dist2_rgrad (colvarvalue const &x1,
inline cvm::real colvar::distance_vec::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::fatal_error ("Error: cannot compare() two distance vectors.\n");
cvm::error ("Error: cannot compare() two distance vectors.\n");
return 0.0;
}
@ -1404,7 +1440,7 @@ inline colvarvalue colvar::distance_dir::dist2_rgrad (colvarvalue const &x1,
inline cvm::real colvar::distance_dir::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::fatal_error ("Error: cannot compare() two distance directions.\n");
cvm::error ("Error: cannot compare() two distance directions.\n");
return 0.0;
}
@ -1431,15 +1467,9 @@ inline colvarvalue colvar::orientation::dist2_rgrad (colvarvalue const &x1,
inline cvm::real colvar::orientation::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::fatal_error ("Error: cannot compare() two quaternions.\n");
cvm::error ("Error: cannot compare() two quaternions.\n");
return 0.0;
}
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

18
lib/colvars/colvarcomp_angles.cpp
View File

@ -1,3 +1,4 @@
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvar.h"
@ -6,7 +7,6 @@
#include <cmath>
colvar::angle::angle (std::string const &conf)
: cvc (conf)
{
@ -75,6 +75,7 @@ void colvar::angle::calc_value()
void colvar::angle::calc_gradients()
{
size_t i;
cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
cvm::real const dxdcos = -1.0 / std::sqrt (1.0 - cos_theta*cos_theta);
@ -84,17 +85,17 @@ void colvar::angle::calc_gradients()
dxdr3 = (180.0/PI) * dxdcos *
(1.0/r23l) * ( r21/r21l + (-1.0) * cos_theta * r23/r23l );
for (size_t i = 0; i < group1.size(); i++) {
for (i = 0; i < group1.size(); i++) {
group1[i].grad = (group1[i].mass/group1.total_mass) *
(dxdr1);
}
for (size_t i = 0; i < group2.size(); i++) {
for (i = 0; i < group2.size(); i++) {
group2[i].grad = (group2[i].mass/group2.total_mass) *
(dxdr1 + dxdr3) * (-1.0);
}
for (size_t i = 0; i < group3.size(); i++) {
for (i = 0; i < group3.size(); i++) {
group3[i].grad = (group3[i].mass/group3.total_mass) *
(dxdr3);
}
@ -307,16 +308,17 @@ void colvar::dihedral::calc_gradients()
+dsindB.y*r34.x - dsindB.x*r34.y);
}
for (size_t i = 0; i < group1.size(); i++)
size_t i;
for (i = 0; i < group1.size(); i++)
group1[i].grad = (group1[i].mass/group1.total_mass) * (-f1);
for (size_t i = 0; i < group2.size(); i++)
for (i = 0; i < group2.size(); i++)
group2[i].grad = (group2[i].mass/group2.total_mass) * (-f2 + f1);
for (size_t i = 0; i < group3.size(); i++)
for (i = 0; i < group3.size(); i++)
group3[i].grad = (group3[i].mass/group3.total_mass) * (-f3 + f2);
for (size_t i = 0; i < group4.size(); i++)
for (i = 0; i < group4.size(); i++)
group4[i].grad = (group4[i].mass/group4.total_mass) * (f3);
}

4
lib/colvars/colvarcomp_coordnums.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include <cmath>
#include "colvarmodule.h"
@ -276,7 +278,7 @@ colvar::h_bond::h_bond()
colvar::h_bond::~h_bond()
{
for (int i=0; i<atom_groups.size(); i++) {
for (unsigned int i=0; i<atom_groups.size(); i++) {
delete atom_groups[i];
}
}

98
lib/colvars/colvarcomp_distances.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include <cmath>
#include "colvarmodule.h"
@ -40,6 +42,7 @@ colvar::distance::distance()
b_inverse_gradients = true;
b_Jacobian_derivative = true;
b_1site_force = false;
b_no_PBC = false;
x.type (colvarvalue::type_scalar);
}
@ -143,8 +146,9 @@ colvar::distance_z::distance_z (std::string const &conf)
b_periodic = true;
if ((wrap_center != 0.0) && (period == 0.0)) {
cvm::fatal_error ("Error: wrapAround was defined in a distanceZ component,"
" but its period has not been set.\n");
cvm::error ("Error: wrapAround was defined in a distanceZ component,"
" but its period has not been set.\n");
return;
}
parse_group (conf, "main", main);
@ -162,8 +166,10 @@ colvar::distance_z::distance_z (std::string const &conf)
cvm::log ("Warning: explicit axis definition will be ignored!");
} else {
if (get_keyval (conf, "axis", axis, cvm::rvector (0.0, 0.0, 1.0))) {
if (axis.norm2() == 0.0)
cvm::fatal_error ("Axis vector is zero!");
if (axis.norm2() == 0.0) {
cvm::error ("Axis vector is zero!");
return;
}
if (axis.norm2() != 1.0) {
axis = axis.unit();
cvm::log ("The normalized axis is: "+cvm::to_str (axis)+".\n");
@ -234,6 +240,15 @@ void colvar::distance_z::calc_gradients()
cvm::position_distance (main.center_of_mass(), ref1.center_of_mass()) + x.real_value * axis ));
}
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients for group main:\n");
debug_gradients (main);
cvm::log ("Debugging gradients for group ref1:\n");
debug_gradients (ref1);
cvm::log ("Debugging gradients for group ref2:\n");
debug_gradients (ref2);
}
}
void colvar::distance_z::calc_force_invgrads()
@ -422,16 +437,19 @@ colvar::distance_inv::distance_inv (std::string const &conf)
function_type = "distance_inv";
get_keyval (conf, "exponent", exponent, 6);
if (exponent%2) {
cvm::fatal_error ("Error: odd exponent provided, can only use even ones.\n");
cvm::error ("Error: odd exponent provided, can only use even ones.\n");
return;
}
if (exponent <= 0) {
cvm::fatal_error ("Error: negative or zero exponent provided.\n");
cvm::error ("Error: negative or zero exponent provided.\n");
return;
}
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
if (ai1->id == ai2->id)
cvm::fatal_error ("Error: group1 and group1 have some atoms in common: this is not allowed for distanceInv.\n");
cvm::error ("Error: group1 and group1 have some atoms in common: this is not allowed for distanceInv.\n");
return;
}
}
@ -640,8 +658,10 @@ colvar::inertia_z::inertia_z (std::string const &conf)
{
function_type = "inertia_z";
if (get_keyval (conf, "axis", axis, cvm::rvector (0.0, 0.0, 1.0))) {
if (axis.norm2() == 0.0)
cvm::fatal_error ("Axis vector is zero!");
if (axis.norm2() == 0.0) {
cvm::error ("Axis vector is zero!");
return;
}
if (axis.norm2() != 1.0) {
axis = axis.unit();
cvm::log ("The normalized axis is: "+cvm::to_str (axis)+".\n");
@ -700,8 +720,10 @@ colvar::rmsd::rmsd (std::string const &conf)
parse_group (conf, "atoms", atoms);
atom_groups.push_back (&atoms);
if (atoms.b_dummy)
cvm::fatal_error ("Error: \"atoms\" cannot be a dummy atom.");
if (atoms.b_dummy) {
cvm::error ("Error: \"atoms\" cannot be a dummy atom.");
return;
}
if (atoms.ref_pos_group != NULL) {
cvm::log ("The option \"refPositionsGroup\" (alternative group for fitting) was enabled: "
@ -715,10 +737,11 @@ colvar::rmsd::rmsd (std::string const &conf)
if (get_keyval (conf, "refPositions", ref_pos, ref_pos)) {
cvm::log ("Using reference positions from configuration file to calculate the variable.\n");
if (ref_pos.size() != atoms.size()) {
cvm::fatal_error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms of group \"atoms\" ("+
cvm::to_str (atoms.size())+").\n");
cvm::error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms of group \"atoms\" ("+
cvm::to_str (atoms.size())+").\n");
return;
}
}
{
@ -726,8 +749,9 @@ colvar::rmsd::rmsd (std::string const &conf)
if (get_keyval (conf, "refPositionsFile", ref_pos_file, std::string (""))) {
if (ref_pos.size()) {
cvm::fatal_error ("Error: cannot specify \"refPositionsFile\" and "
cvm::error ("Error: cannot specify \"refPositionsFile\" and "
"\"refPositions\" at the same time.\n");
return;
}
std::string ref_pos_col;
@ -737,8 +761,9 @@ colvar::rmsd::rmsd (std::string const &conf)
// if provided, use PDB column to select coordinates
bool found = get_keyval (conf, "refPositionsColValue", ref_pos_col_value, 0.0);
if (found && !ref_pos_col_value)
cvm::fatal_error ("Error: refPositionsColValue, "
cvm::error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
return;
} else {
// if not, rely on existing atom indices for the group
atoms.create_sorted_ids();
@ -897,25 +922,30 @@ colvar::eigenvector::eigenvector (std::string const &conf)
if (b_inline) {
cvm::log ("Using reference positions from input file.\n");
if (ref_pos.size() != atoms.size()) {
cvm::fatal_error ("Error: reference positions do not "
cvm::error ("Error: reference positions do not "
"match the number of requested atoms.\n");
return;
}
}
std::string file_name;
if (get_keyval (conf, "refPositionsFile", file_name)) {
if (b_inline)
cvm::fatal_error ("Error: refPositions and refPositionsFile cannot be specified at the same time.\n");
if (b_inline) {
cvm::error ("Error: refPositions and refPositionsFile cannot be specified at the same time.\n");
return;
}
std::string file_col;
double file_col_value;
if (get_keyval (conf, "refPositionsCol", file_col, std::string (""))) {
// use PDB flags if column is provided
bool found = get_keyval (conf, "refPositionsColValue", file_col_value, 0.0);
if (found && !file_col_value)
cvm::fatal_error ("Error: refPositionsColValue, "
if (found && !file_col_value) {
cvm::error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
return;
}
} else {
// if not, use atom indices
atoms.create_sorted_ids();
@ -965,17 +995,20 @@ colvar::eigenvector::eigenvector (std::string const &conf)
std::string file_name;
if (get_keyval (conf, "vectorFile", file_name)) {
if (b_inline)
cvm::fatal_error ("Error: vector and vectorFile cannot be specified at the same time.\n");
if (b_inline) {
cvm::error ("Error: vector and vectorFile cannot be specified at the same time.\n");
return;
}
std::string file_col;
double file_col_value;
if (get_keyval (conf, "vectorCol", file_col, std::string (""))) {
// use PDB flags if column is provided
bool found = get_keyval (conf, "vectorColValue", file_col_value, 0.0);
if (found && !file_col_value)
cvm::fatal_error ("Error: vectorColValue, "
"if provided, must be non-zero.\n");
if (found && !file_col_value) {
cvm::error ("Error: vectorColValue, if provided, must be non-zero.\n");
return;
}
} else {
// if not, use atom indices
atoms.create_sorted_ids();
@ -987,13 +1020,14 @@ colvar::eigenvector::eigenvector (std::string const &conf)
}
if (!ref_pos.size() || !eigenvec.size()) {
cvm::fatal_error ("Error: both reference coordinates"
cvm::error ("Error: both reference coordinates"
"and eigenvector must be defined.\n");
return;
}
cvm::atom_pos eig_center (0.0, 0.0, 0.0);
for (size_t i = 0; i < atoms.size(); i++) {
eig_center += eigenvec[i];
for (size_t eil = 0; eil < atoms.size(); eil++) {
eig_center += eigenvec[eil];
}
eig_center *= 1.0 / atoms.size();
cvm::log ("Geometric center of the provided vector: "+cvm::to_str (eig_center)+"\n");
@ -1038,8 +1072,8 @@ colvar::eigenvector::eigenvector (std::string const &conf)
// for inverse gradients
eigenvec_invnorm2 = 0.0;
for (size_t i = 0; i < atoms.size(); i++) {
eigenvec_invnorm2 += eigenvec[i].norm2();
for (size_t ein = 0; ein < atoms.size(); ein++) {
eigenvec_invnorm2 += eigenvec[ein].norm2();
}
eigenvec_invnorm2 = 1.0 / eigenvec_invnorm2;

7
lib/colvars/colvarcomp_protein.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include <cmath>
#include "colvarmodule.h"
@ -162,10 +164,11 @@ void colvar::alpha_angles::calc_value()
void colvar::alpha_angles::calc_gradients()
{
for (size_t i = 0; i < theta.size(); i++)
size_t i;
for (i = 0; i < theta.size(); i++)
(theta[i])->calc_gradients();
for (size_t i = 0; i < hb.size(); i++)
for (i = 0; i < hb.size(); i++)
(hb[i])->calc_gradients();
}

59
lib/colvars/colvarcomp_rotations.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include <cmath>
#include "colvarmodule.h"
@ -57,11 +59,12 @@ colvar::orientation::orientation (std::string const &conf)
"assumed that each atom is the closest "
"periodic image to the center of geometry.\n");
cvm::rvector cog (0.0, 0.0, 0.0);
for (size_t i = 0; i < ref_pos.size(); i++) {
size_t i;
for (i = 0; i < ref_pos.size(); i++) {
cog += ref_pos[i];
}
cog /= cvm::real (ref_pos.size());
for (size_t i = 0; i < ref_pos.size(); i++) {
for (i = 0; i < ref_pos.size(); i++) {
ref_pos[i] -= cog;
}
@ -167,10 +170,61 @@ void colvar::orientation_angle::calc_gradients()
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
}
if (b_debug_gradients) {
cvm::log ("Debugging orientationAngle component gradients:\n");
debug_gradients (atoms);
}
}
void colvar::orientation_angle::apply_force (colvarvalue const &force)
{
cvm::real const &fw = force.real_value;
if (!atoms.noforce) {
atoms.apply_colvar_force (fw);
}
}
colvar::orientation_proj::orientation_proj (std::string const &conf)
: orientation (conf)
{
function_type = "orientation_proj";
x.type (colvarvalue::type_scalar);
}
colvar::orientation_proj::orientation_proj()
: orientation()
{
function_type = "orientation_proj";
x.type (colvarvalue::type_scalar);
}
void colvar::orientation_proj::calc_value()
{
atoms_cog = atoms.center_of_geometry();
rot.calc_optimal_rotation (ref_pos, atoms.positions_shifted (-1.0 * atoms_cog));
x.real_value = 2.0 * (rot.q).q0 * (rot.q).q0 - 1.0;
}
void colvar::orientation_proj::calc_gradients()
{
cvm::real const dxdq0 = 2.0 * 2.0 * (rot.q).q0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
}
if (b_debug_gradients) {
cvm::log ("Debugging orientationProj component gradients:\n");
debug_gradients (atoms);
}
}
void colvar::orientation_proj::apply_force (colvarvalue const &force)
{
cvm::real const &fw = force.real_value;
@ -180,6 +234,7 @@ void colvar::orientation_angle::apply_force (colvarvalue const &force)
}
colvar::tilt::tilt (std::string const &conf)
: orientation (conf)
{

2
lib/colvars/colvargrid.cpp
View File

@ -1,4 +1,4 @@
// -*- c++ -*-
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"

406
lib/colvars/colvargrid.h
View File

@ -1,4 +1,4 @@
// -*- c++ -*-
/// -*- c++ -*-
#ifndef COLVARGRID_H
#define COLVARGRID_H
@ -55,8 +55,10 @@ protected:
for (size_t i = 0; i < nd; i++) {
addr += ix[i]*nxc[i];
if (cvm::debug()) {
if (ix[i] >= nx[i])
cvm::fatal_error ("Error: exceeding bounds in colvar_grid.\n");
if (ix[i] >= nx[i]) {
cvm::error ("Error: exceeding bounds in colvar_grid.\n");
return 0;
}
}
}
return addr;
@ -135,9 +137,11 @@ public:
nt = mult;
for (int i = nd-1; i >= 0; i--) {
if (nx_i[i] <= 0)
cvm::fatal_error ("Error: providing an invalid number of points, "+
if (nx_i[i] <= 0) {
cvm::error ("Error: providing an invalid number of points, "+
cvm::to_str (nx_i[i])+".\n");
return;
}
nxc[i] = nt;
nt *= nx[i];
}
@ -220,20 +224,23 @@ public:
for (size_t i = 0; i < cv.size(); i++) {
if (cv[i]->type() != colvarvalue::type_scalar) {
cvm::fatal_error ("Colvar grids can only be automatically "
"constructed for scalar variables. "
"ABF and histogram can not be used; metadynamics "
"can be used with useGrids disabled.\n");
cvm::error ("Colvar grids can only be automatically "
"constructed for scalar variables. "
"ABF and histogram can not be used; metadynamics "
"can be used with useGrids disabled.\n");
return;
}
if (cv[i]->width <= 0.0) {
cvm::fatal_error ("Tried to initialize a grid on a "
cvm::error ("Tried to initialize a grid on a "
"variable with negative or zero width.\n");
return;
}
if (!cv[i]->tasks[colvar::task_lower_boundary] || !cv[i]->tasks[colvar::task_upper_boundary]) {
cvm::fatal_error ("Tried to initialize a grid on a "
"variable with undefined boundaries.\n");
cvm::error ("Tried to initialize a grid on a "
"variable with undefined boundaries.\n");
return;
}
widths.push_back (cv[i]->width);
@ -303,8 +310,9 @@ public:
ix[i] = (ix[i] + nx[i]) % nx[i]; //to ensure non-negative result
} else {
if (ix[i] < 0 || ix[i] >= nx[i])
cvm::fatal_error ("Trying to wrap illegal index vector (non-PBC): "
+ cvm::to_str (ix));
cvm::error ("Trying to wrap illegal index vector (non-PBC): "
+ cvm::to_str (ix));
return;
}
}
}
@ -437,9 +445,11 @@ public:
/// of whether it fits or not.
void map_grid (colvar_grid<T> const &other_grid)
{
if (other_grid.multiplicity() != this->multiplicity())
cvm::fatal_error ("Error: trying to merge two grids with values of "
if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error ("Error: trying to merge two grids with values of "
"different multiplicity.\n");
return;
}
std::vector<colvarvalue> const &gb = this->lower_boundaries;
std::vector<cvm::real> const &gw = this->widths;
@ -479,9 +489,11 @@ public:
void add_grid (colvar_grid<T> const &other_grid,
cvm::real scale_factor = 1.0)
{
if (other_grid.multiplicity() != this->multiplicity())
cvm::fatal_error ("Error: trying to sum togetehr two grids with values of "
if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error ("Error: trying to sum togetehr two grids with values of "
"different multiplicity.\n");
return;
}
if (scale_factor != 1.0)
for (size_t i = 0; i < data.size(); i++) {
data[i] += scale_factor * other_grid.data[i];
@ -570,25 +582,26 @@ public:
/// \brief Write the grid parameters (number of colvars, boundaries, width and number of points)
std::ostream & write_params (std::ostream &os)
{
size_t i;
os << "grid_parameters {\n n_colvars " << nd << "\n";
os << " lower_boundaries ";
for (size_t i = 0; i < nd; i++)
for (i = 0; i < nd; i++)
os << " " << lower_boundaries[i];
os << "\n";
os << " upper_boundaries ";
for (size_t i = 0; i < nd; i++)
for (i = 0; i < nd; i++)
os << " " << upper_boundaries[i];
os << "\n";
os << " widths ";
for (size_t i = 0; i < nd; i++)
for (i = 0; i < nd; i++)
os << " " << widths[i];
os << "\n";
os << " sizes ";
for (size_t i = 0; i < nd; i++)
for (i = 0; i < nd; i++)
os << " " << nx[i];
os << "\n";
@ -605,12 +618,14 @@ public:
{
size_t nd_in = 0;
colvarparse::get_keyval (conf, "n_colvars", nd_in, nd, colvarparse::parse_silent);
if (nd_in != nd)
cvm::fatal_error ("Error: trying to read data for a grid "
"that contains a different number of colvars ("+
cvm::to_str (nd_in)+") than the grid defined "
"in the configuration file ("+cvm::to_str (nd)+
").\n");
if (nd_in != nd) {
cvm::error ("Error: trying to read data for a grid "
"that contains a different number of colvars ("+
cvm::to_str (nd_in)+") than the grid defined "
"in the configuration file ("+cvm::to_str (nd)+
").\n");
return false;
}
}
colvarparse::get_keyval (conf, "lower_boundaries",
@ -653,8 +668,9 @@ public:
upper_boundaries[i])) > 1.0E-10) ||
(std::sqrt (cv[i]->dist2 (cv[i]->width,
widths[i])) > 1.0E-10) ) {
cvm::fatal_error ("Error: restart information for a grid is "
"inconsistent with that of its colvars.\n");
cvm::error ("Error: restart information for a grid is "
"inconsistent with that of its colvars.\n");
return;
}
}
}
@ -675,9 +691,10 @@ public:
(std::fabs (other_grid.widths[i] -
widths[i]) > 1.0E-10) ||
(data.size() != other_grid.data.size()) ) {
cvm::fatal_error ("Error: inconsistency between "
"two grids that are supposed to be equal, "
"aside from the data stored.\n");
cvm::error ("Error: inconsistency between "
"two grids that are supposed to be equal, "
"aside from the data stored.\n");
return;
}
}
}
@ -710,169 +727,167 @@ public:
return os;
}
/// \brief Read data written by colvar_grid::write_raw()
std::istream & read_raw (std::istream &is)
{
size_t const start_pos = is.tellg();
for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix)) {
for (size_t imult = 0; imult < mult; imult++) {
T new_value;
if (is >> new_value) {
value_input (ix, new_value, imult);
} else {
is.clear();
is.seekg (start_pos, std::ios::beg);
is.setstate (std::ios::failbit);
return is;
}
}
}
has_data = true;
return is;
}
/// \brief To be called after colvar_grid::read_raw() returns an error
void read_raw_error()
{
cvm::fatal_error ("Error: failed to read all of the grid points from file. Possible explanations: grid parameters in the configuration (lowerBoundary, upperBoundary, width) are different from those in the file, or the file is corrupt/incomplete.\n");
}
/// \brief Write the grid in a format which is both human readable
/// and suitable for visualization e.g. with gnuplot
void write_multicol (std::ostream &os)
{
std::streamsize const w = os.width();
std::streamsize const p = os.precision();
// Data in the header: nColvars, then for each
// xiMin, dXi, nPoints, periodic
os << std::setw (2) << "# " << nd << "\n";
for (size_t i = 0; i < nd; i++) {
os << "# "
<< std::setw (10) << lower_boundaries[i]
<< std::setw (10) << widths[i]
<< std::setw (10) << nx[i] << " "
<< periodic[i] << "\n";
}
for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix) ) {
if (ix.back() == 0) {
// if the last index is 0, add a new line to mark the new record
os << "\n";
}
for (size_t i = 0; i < nd; i++) {
os << " "
<< std::setw (w) << std::setprecision (p)
<< bin_to_value_scalar (ix[i], i);
}
os << " ";
for (size_t imult = 0; imult < mult; imult++) {
os << " "
<< std::setw (w) << std::setprecision (p)
<< value_output (ix, imult);
}
os << "\n";
}
}
/// \brief Read a grid written by colvar_grid::write_multicol()
/// Adding data if add is true, replacing if false
std::istream & read_multicol (std::istream &is, bool add = false)
{
// Data in the header: nColvars, then for each
// xiMin, dXi, nPoints, periodic
std::string hash;
cvm::real lower, width, x;
size_t n, periodic;
bool remap;
std::vector<T> new_value;
std::vector<int> nx_read;
std::vector<int> bin;
if ( cv.size() != nd ) {
cvm::fatal_error ("Cannot read grid file: missing reference to colvars.");
}
if ( !(is >> hash) || (hash != "#") ) {
cvm::fatal_error ("Error reading grid at position "+
cvm::to_str (is.tellg())+" in stream (read \"" + hash + "\")\n");
}
is >> n;
if ( n != nd ) {
cvm::fatal_error ("Error reading grid: wrong number of collective variables.\n");
}
nx_read.resize (n);
bin.resize (n);
new_value.resize (mult);
if (this->has_parent_data && add) {
new_data.resize (data.size());
}
remap = false;
for (size_t i = 0; i < nd; i++ ) {
if ( !(is >> hash) || (hash != "#") ) {
cvm::fatal_error ("Error reading grid at position "+
cvm::to_str (is.tellg())+" in stream (read \"" + hash + "\")\n");
}
is >> lower >> width >> nx_read[i] >> periodic;
if ( (std::fabs (lower - lower_boundaries[i].real_value) > 1.0e-10) ||
(std::fabs (width - widths[i] ) > 1.0e-10) ||
(nx_read[i] != nx[i]) ) {
cvm::log ("Warning: reading from different grid definition (colvar "
+ cvm::to_str (i+1) + "); remapping data on new grid.\n");
remap = true;
}
}
if ( remap ) {
// re-grid data
while (is.good()) {
bool end_of_file = false;
for (size_t i = 0; i < nd; i++ ) {
if ( !(is >> x) ) end_of_file = true;
bin[i] = value_to_bin_scalar (x, i);
}
if (end_of_file) break;
/// \brief Read data written by colvar_grid::write_raw()
std::istream & read_raw (std::istream &is)
{
size_t const start_pos = is.tellg();
for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix)) {
for (size_t imult = 0; imult < mult; imult++) {
is >> new_value[imult];
}
if ( index_ok(bin) ) {
for (size_t imult = 0; imult < mult; imult++) {
value_input (bin, new_value[imult], imult, add);
T new_value;
if (is >> new_value) {
value_input (ix, new_value, imult);
} else {
is.clear();
is.seekg (start_pos, std::ios::beg);
is.setstate (std::ios::failbit);
cvm::error ("Error: failed to read all of the grid points from file. Possible explanations: grid parameters in the configuration (lowerBoundary, upperBoundary, width) are different from those in the file, or the file is corrupt/incomplete.\n");
return is;
}
}
}
} else {
// do not re-grid the data but assume the same grid is used
has_data = true;
return is;
}
/// \brief Write the grid in a format which is both human readable
/// and suitable for visualization e.g. with gnuplot
void write_multicol (std::ostream &os)
{
std::streamsize const w = os.width();
std::streamsize const p = os.precision();
// Data in the header: nColvars, then for each
// xiMin, dXi, nPoints, periodic
os << std::setw (2) << "# " << nd << "\n";
for (size_t i = 0; i < nd; i++) {
os << "# "
<< std::setw (10) << lower_boundaries[i]
<< std::setw (10) << widths[i]
<< std::setw (10) << nx[i] << " "
<< periodic[i] << "\n";
}
for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix) ) {
for (size_t i = 0; i < nd; i++ ) {
is >> x;
if (ix.back() == 0) {
// if the last index is 0, add a new line to mark the new record
os << "\n";
}
for (size_t i = 0; i < nd; i++) {
os << " "
<< std::setw (w) << std::setprecision (p)
<< bin_to_value_scalar (ix[i], i);
}
os << " ";
for (size_t imult = 0; imult < mult; imult++) {
is >> new_value[imult];
value_input (ix, new_value[imult], imult, add);
os << " "
<< std::setw (w) << std::setprecision (p)
<< value_output (ix, imult);
}
os << "\n";
}
}
has_data = true;
return is;
}
/// \brief Read a grid written by colvar_grid::write_multicol()
/// Adding data if add is true, replacing if false
std::istream & read_multicol (std::istream &is, bool add = false)
{
// Data in the header: nColvars, then for each
// xiMin, dXi, nPoints, periodic
std::string hash;
cvm::real lower, width, x;
size_t n, periodic;
bool remap;
std::vector<T> new_value;
std::vector<int> nx_read;
std::vector<int> bin;
if ( cv.size() != nd ) {
cvm::error ("Cannot read grid file: missing reference to colvars.");
return is;
}
if ( !(is >> hash) || (hash != "#") ) {
cvm::error ("Error reading grid at position "+
cvm::to_str (is.tellg())+" in stream (read \"" + hash + "\")\n");
return is;
}
is >> n;
if ( n != nd ) {
cvm::error ("Error reading grid: wrong number of collective variables.\n");
return is;
}
nx_read.resize (n);
bin.resize (n);
new_value.resize (mult);
if (this->has_parent_data && add) {
new_data.resize (data.size());
}
remap = false;
for (size_t i = 0; i < nd; i++ ) {
if ( !(is >> hash) || (hash != "#") ) {
cvm::error ("Error reading grid at position "+
cvm::to_str (is.tellg())+" in stream (read \"" + hash + "\")\n");
return is;
}
is >> lower >> width >> nx_read[i] >> periodic;
if ( (std::fabs (lower - lower_boundaries[i].real_value) > 1.0e-10) ||
(std::fabs (width - widths[i] ) > 1.0e-10) ||
(nx_read[i] != nx[i]) ) {
cvm::log ("Warning: reading from different grid definition (colvar "
+ cvm::to_str (i+1) + "); remapping data on new grid.\n");
remap = true;
}
}
if ( remap ) {
// re-grid data
while (is.good()) {
bool end_of_file = false;
for (size_t i = 0; i < nd; i++ ) {
if ( !(is >> x) ) end_of_file = true;
bin[i] = value_to_bin_scalar (x, i);
}
if (end_of_file) break;
for (size_t imult = 0; imult < mult; imult++) {
is >> new_value[imult];
}
if ( index_ok(bin) ) {
for (size_t imult = 0; imult < mult; imult++) {
value_input (bin, new_value[imult], imult, add);
}
}
}
} else {
// do not re-grid the data but assume the same grid is used
for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix) ) {
for (size_t i = 0; i < nd; i++ ) {
is >> x;
}
for (size_t imult = 0; imult < mult; imult++) {
is >> new_value[imult];
value_input (ix, new_value[imult], imult, add);
}
}
}
has_data = true;
return is;
}
};
@ -981,8 +996,11 @@ public:
{
cvm::real A0, A1;
std::vector<int> ix;
if (nd != 2) cvm::fatal_error ("Finite differences available in dimension 2 only.");
for (int n = 0; n < nd; n++) {
if (nd != 2) {
cvm::error ("Finite differences available in dimension 2 only.");
return grad;
}
for (unsigned int n = 0; n < nd; n++) {
ix = ix0;
A0 = data[address (ix)];
ix[n]++; wrap (ix);
@ -1001,9 +1019,11 @@ public:
virtual cvm::real value_output (std::vector<int> const &ix,
size_t const &imult = 0)
{
if (imult > 0)
cvm::fatal_error ("Error: trying to access a component "
"larger than 1 in a scalar data grid.\n");
if (imult > 0) {
cvm::error ("Error: trying to access a component "
"larger than 1 in a scalar data grid.\n");
return 0.;
}
if (samples)
return (samples->value (ix) > 0) ?
(data[address (ix)] / cvm::real (samples->value (ix))) :
@ -1020,9 +1040,11 @@ public:
size_t const &imult = 0,
bool add = false)
{
if (imult > 0)
cvm::fatal_error ("Error: trying to access a component "
"larger than 1 in a scalar data grid.\n");
if (imult > 0) {
cvm::error ("Error: trying to access a component "
"larger than 1 in a scalar data grid.\n");
return;
}
if (add) {
if (samples)
data[address (ix)] += new_value * samples->new_count (ix);

1511
lib/colvars/colvarmodule.cpp
View File

File diff suppressed because it is too large Load Diff

159
lib/colvars/colvarmodule.h
View File

@ -1,8 +1,10 @@
/// -*- c++ -*-
#ifndef COLVARMODULE_H
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2014-08-13"
#define COLVARS_VERSION "2014-10-07"
#endif
#ifndef COLVARS_DEBUG
@ -18,6 +20,19 @@
/// shared between all object instances) to be accessed from other
/// objects.
// Internal method return codes
#define COLVARS_ERROR -1
#define COLVARS_OK 0
// On error, values of the colvars module error register
#define GENERAL_ERROR 1
#define FILE_ERROR (1<<1)
#define MEMORY_ERROR (1<<2)
#define BUG_ERROR (1<<3) // Inconsistent state indicating bug
#define INPUT_ERROR (1<<4) // out of bounds or inconsistent input
#define DELETE_COLVARS (1<<5) // Instruct the caller to delete cvm
#define FATAL_ERROR (1<<6) // Should be set, or not, together with other bits
#include <iostream>
#include <iomanip>
@ -34,6 +49,7 @@ class colvarparse;
class colvar;
class colvarbias;
class colvarproxy;
class colvarscript;
/// \brief Collective variables module (main class)
@ -55,6 +71,8 @@ private:
public:
friend class colvarproxy;
// TODO colvarscript should be unaware of colvarmodule's internals
friend class colvarscript;
/// Defining an abstract real number allows to switch precision
typedef double real;
@ -85,6 +103,22 @@ public:
typedef std::vector<atom>::iterator atom_iter;
typedef std::vector<atom>::const_iterator atom_const_iter;
/// Module-wide error state
/// see constants at the top of this file
static int errorCode;
static inline void set_error_bits(int code)
{
errorCode |= code;
}
static inline int get_error()
{
return errorCode;
}
static inline void clear_error()
{
errorCode = 0;
}
/// Current step number
static size_t it;
/// Starting step number for this run
@ -115,9 +149,6 @@ public:
/// Prefix for all output files for this run
static std::string output_prefix;
/// Prefix for files from a previous run (including restart/output)
static std::string input_prefix;
/// input restart file name (determined from input_prefix)
static std::string restart_in_name;
@ -158,26 +189,79 @@ public:
/// \brief Constructor \param config_name Configuration file name
/// \param restart_name (optional) Restart file name
colvarmodule (char const *config_name,
colvarproxy *proxy_in);
colvarmodule (colvarproxy *proxy);
/// Destructor
~colvarmodule();
/// Initialize collective variables
void init_colvars (std::string const &conf);
/// Actual function called by the destructor
int reset();
/// Initialize collective variable biases
void init_biases (std::string const &conf);
/// Open a config file, load its contents, and pass it to config_string()
int config_file (char const *config_file_name);
/// Re-initialize data at the beginning of a run. For use with
/// MD codes that can change system parameters like atom masses
/// between run commands.
void setup();
/// \brief Parse a config string assuming it is a complete configuration
/// (i.e. calling all parse functions)
int config_string (std::string const &conf);
/// \brief Parse a "clean" config string (no comments)
int config (std::string &conf);
// Parse functions (setup internal data based on a string)
/// Parse the few module's global parameters
int parse_global_params (std::string const &conf);
/// Parse and initialize collective variables
int parse_colvars (std::string const &conf);
/// Parse and initialize collective variable biases
int parse_biases (std::string const &conf);
// "Setup" functions (change internal data based on related data
// from the proxy that may change during program execution)
// No additional parsing is done within these functions
/// (Re)initialize internal data (currently used by LAMMPS)
/// Also calls setup() member functions of colvars and biases
int setup();
/// (Re)initialize and (re)read the input state file calling read_restart()
int setup_input();
/// (Re)initialize the output trajectory and state file (does not write it yet)
int setup_output();
/// Read the input restart file
std::istream & read_restart (std::istream &is);
/// Write the output restart file
std::ostream & write_restart (std::ostream &os);
/// Open a trajectory file if requested (and leave it open)
int open_traj_file (std::string const &file_name);
/// Close it
int close_traj_file();
/// Write in the trajectory file
std::ostream & write_traj (std::ostream &os);
/// Write explanatory labels in the trajectory file
std::ostream & write_traj_label (std::ostream &os);
/// Write all FINAL output files
int write_output_files();
/// Backup a file before writing it
static int backup_file (char const *filename);
/// Look up a bias by name; returns NULL if not found
static colvarbias * bias_by_name(std::string const &name);
/// Look up a colvar by name; returns NULL if not found
static colvar * colvar_by_name(std::string const &name);
/// Load new configuration for the given bias -
/// currently works for harmonic (force constant and/or centers)
void change_configuration (std::string const &bias_name, std::string const &conf);
int change_configuration (std::string const &bias_name, std::string const &conf);
/// Read a colvar value
std::string read_colvar(std::string const &name);
@ -187,27 +271,16 @@ public:
real energy_difference (std::string const &bias_name, std::string const &conf);
/// Calculate collective variables and biases
void calc();
/// Read the input restart file
std::istream & read_restart (std::istream &is);
/// Write the output restart file
std::ostream & write_restart (std::ostream &os);
/// Write all output files (called by the proxy)
void write_output_files();
/// \brief Call colvarproxy::backup_file()
static void backup_file (char const *filename);
int calc();
/// Perform analysis
void analyze();
int analyze();
/// \brief Read a collective variable trajectory (post-processing
/// only, not called at runtime)
bool read_traj (char const *traj_filename,
int read_traj (char const *traj_filename,
size_t traj_read_begin,
size_t traj_read_end);
/// Get the pointer of a colvar from its name (returns NULL if not found)
static colvar * colvar_p (std::string const &name);
/// Quick conversion of an object to a string
template<typename T> static std::string to_str (T const &x,
size_t const &width = 0,
@ -267,6 +340,9 @@ public:
/// Print a message to the main log and exit with error code
static void fatal_error (std::string const &message);
/// Print a message to the main log and set global error code
static void error (std::string const &message, int code = GENERAL_ERROR);
/// Print a message to the main log and exit normally
static void exit (std::string const &message);
@ -307,21 +383,21 @@ public:
static std::list<std::vector<int> > index_groups;
/// \brief Read a Gromacs .ndx file
static void read_index_file (char const *filename);
static int read_index_file (char const *filename);
/// \brief Create atoms from a file \param filename name of the file
/// (usually a PDB) \param atoms array of the atoms to be allocated
/// \param pdb_field (optiona) if "filename" is a PDB file, use this
/// field to determine which are the atoms to be set
static void load_atoms (char const *filename,
static int load_atoms (char const *filename,
std::vector<atom> &atoms,
std::string const &pdb_field,
double const pdb_field_value = 0.0);
/// \brief Load the coordinates for a group of atoms from a file
/// (PDB or XYZ)
static void load_coords (char const *filename,
static int load_coords (char const *filename,
std::vector<atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field,
@ -329,7 +405,7 @@ public:
/// \brief Load the coordinates for a group of atoms from an
/// XYZ file
static void load_coords_xyz (char const *filename,
static int load_coords_xyz (char const *filename,
std::vector<atom_pos> &pos,
const std::vector<int> &indices);
@ -366,15 +442,18 @@ protected:
/// Output restart file
std::ofstream restart_out_os;
/// \brief Counter for the current depth in the object hierarchy (useg e.g. in output
static size_t depth;
/// Use scripted colvars forces?
bool use_scripted_forces;
public:
/// \brief Pointer to the proxy object, used to retrieve atomic data
/// from the hosting program; it is static in order to be accessible
/// from static functions in the colvarmodule class
static colvarproxy *proxy;
/// \brief Counter for the current depth in the object hierarchy (useg e.g. in outpu
static size_t depth;
public:
/// Increase the depth (number of indentations in the output)
static void increase_depth();
@ -489,9 +568,3 @@ inline cvm::real cvm::rand_gaussian (void)
}
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

51
lib/colvars/colvarparse.cpp
View File

@ -1,14 +1,13 @@
/// -*- c++ -*-
#include <sstream>
#include <iostream>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
// space & tab
std::string const colvarparse::white_space = " \t";
@ -51,8 +50,8 @@ size_t colvarparse::dummy_pos = 0;
if (is >> x) \
value = x; \
else \
cvm::fatal_error ("Error: in parsing \""+ \
std::string (key)+"\".\n"); \
cvm::error ("Error: in parsing \""+ \
std::string (key)+"\".\n", INPUT_ERROR); \
if (parse_mode != parse_silent) { \
cvm::log ("# "+std::string (key)+" = "+ \
cvm::to_str (value)+"\n"); \
@ -60,8 +59,8 @@ size_t colvarparse::dummy_pos = 0;
} else { \
\
if (b_found_any) \
cvm::fatal_error ("Error: improper or missing value " \
"for \""+std::string (key)+"\".\n"); \
cvm::error ("Error: improper or missing value " \
"for \""+std::string (key)+"\".\n", INPUT_ERROR); \
value = def_value; \
if (parse_mode != parse_silent) { \
cvm::log ("# "+std::string (key)+" = \""+ \
@ -112,9 +111,9 @@ size_t colvarparse::dummy_pos = 0;
cvm::fatal_error ("Error: in parsing \""+ \
std::string (key)+"\".\n"); \
if (data_count > 1) \
cvm::fatal_error ("Error: multiple values " \
"are not allowed for keyword \""+ \
std::string (key)+"\".\n"); \
cvm::error ("Error: multiple values " \
"are not allowed for keyword \""+ \
std::string (key)+"\".\n", INPUT_ERROR); \
if (parse_mode != parse_silent) { \
cvm::log ("# "+std::string (key)+" = "+ \
cvm::to_str (value)+"\n"); \
@ -122,8 +121,8 @@ size_t colvarparse::dummy_pos = 0;
} else { \
\
if (b_found_any) \
cvm::fatal_error ("Error: improper or missing value " \
"for \""+std::string (key)+"\".\n"); \
cvm::error ("Error: improper or missing value " \
"for \""+std::string (key)+"\".\n", INPUT_ERROR); \
value = def_value; \
if (parse_mode != parse_silent) { \
cvm::log ("# "+std::string (key)+" = "+ \
@ -189,8 +188,8 @@ size_t colvarparse::dummy_pos = 0;
if (is >> x) \
values[i] = x; \
else \
cvm::fatal_error ("Error: in parsing \""+ \
std::string (key)+"\".\n"); \
cvm::error ("Error: in parsing \""+ \
std::string (key)+"\".\n", INPUT_ERROR); \
} \
} \
\
@ -202,8 +201,8 @@ size_t colvarparse::dummy_pos = 0;
} else { \
\
if (b_found_any) \
cvm::fatal_error ("Error: improper or missing values for \""+ \
std::string (key)+"\".\n"); \
cvm::error ("Error: improper or missing values for \""+ \
std::string (key)+"\".\n", INPUT_ERROR); \
\
for (size_t i = 0; i < values.size(); i++) \
values[i] = def_values[ (i > def_values.size()) ? 0 : i ]; \
@ -267,7 +266,6 @@ bool colvarparse::get_keyval (std::string const &conf,
std::string (key)+"\".\n");
if (data.size()) {
std::istringstream is (data);
if ( (data == std::string ("on")) ||
(data == std::string ("yes")) ||
(data == std::string ("true")) ) {
@ -349,7 +347,7 @@ void colvarparse::strip_values (std::string &conf)
}
void colvarparse::check_keywords (std::string &conf, char const *key)
int colvarparse::check_keywords (std::string &conf, char const *key)
{
if (cvm::debug())
cvm::log ("Configuration string for \""+std::string (key)+
@ -383,10 +381,17 @@ void colvarparse::check_keywords (std::string &conf, char const *key)
break;
}
}
if (!found_keyword)
cvm::fatal_error ("Error: keyword \""+uk+"\" is not supported, "
if (!found_keyword) {
cvm::log ("Error: keyword \""+uk+"\" is not supported, "
"or not recognized in this context.\n");
cvm::set_error_bits(INPUT_ERROR);
return COLVARS_ERROR;
}
}
allowed_keywords.clear();
data_begin_pos.clear();
data_end_pos.clear();
return COLVARS_OK;
}
@ -635,9 +640,3 @@ bool colvarparse::brace_check (std::string const &conf,
else
return true;
}
// Emacs
// Local Variables:
// mode: C++
// End:

9
lib/colvars/colvarparse.h
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#ifndef COLVARPARSE_H
#define COLVARPARSE_H
@ -125,7 +127,7 @@ public:
/// \brief Check that all the keywords within "conf" are in the list
/// of allowed keywords; this will invoke strip_values() first and
/// then loop over all words
void check_keywords (std::string &conf, char const *key);
int check_keywords (std::string &conf, char const *key);
/// \brief Return a lowercased copy of the string
@ -194,8 +196,3 @@ public:
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

100
lib/colvars/colvarproxy.h
View File

@ -1,24 +1,46 @@
/// -*- c++ -*-
#ifndef COLVARPROXY_H
#define COLVARPROXY_H
#ifndef COLVARPROXY_VERSION
#define COLVARPROXY_VERSION "2014-09-19"
#endif
#include "colvarmodule.h"
#include "colvarvalue.h"
/// \brief Interface class between the collective variables module and
/// the simulation program
// return values for the frame() routine
#define COLVARS_NO_SUCH_FRAME -1
#define COLVARS_NOT_IMPLEMENTED -2
// forward declarations
class colvarscript;
/// \brief Interface between the collective variables module and
/// the simulation or analysis program.
/// This is the base class: each program is supported by a derived class.
/// Only pure virtual functions ("= 0") must be reimplemented in a new interface.
class colvarproxy {
public:
/// Pointer to the instance of colvarmodule
/// Pointer to the main object
colvarmodule *colvars;
/// Default constructor
inline colvarproxy() : script (NULL) {}
/// Default destructor
virtual inline ~colvarproxy() {}
/// (Re)initialize member data after construction
virtual void setup() {}
// **************** SYSTEM-WIDE PHYSICAL QUANTITIES ****************
@ -38,19 +60,38 @@ public:
/// \brief Pseudo-random number with Gaussian distribution
virtual cvm::real rand_gaussian (void) = 0;
/// \brief Get the current frame number
virtual int frame() { return COLVARS_NOT_IMPLEMENTED; }
/// \brief Set the current frame number
// return 0 on success, -1 on failure
virtual int frame (int) { return COLVARS_NOT_IMPLEMENTED; }
// **************** SIMULATION PARAMETERS ****************
/// \brief Prefix to be used for input files (restarts, not
/// configuration)
virtual std::string input_prefix() = 0;
std::string input_prefix_str, output_prefix_str, restart_output_prefix_str;
inline std::string input_prefix()
{
return input_prefix_str;
}
/// \brief Prefix to be used for output restart files
virtual std::string restart_output_prefix() = 0;
inline std::string restart_output_prefix()
{
return restart_output_prefix_str;
}
/// \brief Prefix to be used for output files (final system
/// configuration)
virtual std::string output_prefix() = 0;
inline std::string output_prefix()
{
return output_prefix_str;
}
/// \brief Restarts will be fritten each time this number of steps has passed
virtual size_t restart_frequency() = 0;
@ -91,13 +132,39 @@ public:
void select_closest_images (std::vector<cvm::atom_pos> &pos,
cvm::atom_pos const &ref_pos);
// **************** SCRIPTING INTERFACE ****************
/// Pointer to the scripting interface object
/// (does not need to be allocated in a new interface)
colvarscript *script;
/// is a user force script defined?
bool force_script_defined;
/// Do we have a scripting interface?
bool have_scripts;
/// Run a user-defined colvar forces script
virtual int run_force_callback() { return COLVARS_NOT_IMPLEMENTED; }
virtual int run_colvar_callback(std::string const &name,
std::vector<const colvarvalue *> const &cvcs,
colvarvalue &value)
{ return COLVARS_NOT_IMPLEMENTED; }
virtual int run_colvar_gradient_callback(std::string const &name,
std::vector<const colvarvalue *> const &cvcs,
std::vector<colvarvalue> &gradient)
{ return COLVARS_NOT_IMPLEMENTED; }
// **************** INPUT/OUTPUT ****************
/// Print a message to the main log
virtual void log (std::string const &message) = 0;
/// Print a message to the main log and let the rest of the program handle the error
virtual void error (std::string const &message) = 0;
/// Print a message to the main log and exit with error code
virtual void fatal_error (std::string const &message) = 0;
@ -109,23 +176,23 @@ public:
/// from "filename" will be appended \param pdb_field (optiona) if
/// "filename" is a PDB file, use this field to determine which are
/// the atoms to be set
virtual void load_atoms (char const *filename,
virtual int load_atoms (char const *filename,
std::vector<cvm::atom> &atoms,
std::string const pdb_field,
double const pdb_field_value = 0.0) {}
std::string const &pdb_field,
double const pdb_field_value = 0.0) = 0;
/// \brief Load the coordinates for a group of atoms from a file
/// (usually a PDB); if "pos" is already allocated, the number of its
/// elements must match the number of atoms in "filename"
virtual void load_coords (char const *filename,
virtual int load_coords (char const *filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const pdb_field,
std::string const &pdb_field,
double const pdb_field_value = 0.0) = 0;
/// \brief Rename the given file, before overwriting it
virtual void backup_file (char const *filename) {}
virtual int backup_file (char const *filename)
{ return COLVARS_NOT_IMPLEMENTED; }
};
@ -133,7 +200,7 @@ inline void colvarproxy::select_closest_images (std::vector<cvm::atom_pos> &pos,
cvm::atom_pos const &ref_pos)
{
for (std::vector<cvm::atom_pos>::iterator pi = pos.begin();
pi != pos.end(); pi++) {
pi != pos.end(); ++pi) {
select_closest_image (*pi, ref_pos);
}
}
@ -146,8 +213,3 @@ inline cvm::real colvarproxy::position_dist2 (cvm::atom_pos const &pos1,
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

29
lib/colvars/colvartypes.h
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#ifndef COLVARTYPES_H
#define COLVARTYPES_H
@ -35,7 +37,7 @@ public:
{}
/// \brief Set all components to a scalar value
inline void set (cvm::real const value = 0.0) {
inline void set (cvm::real const &value = 0.0) {
x = y = z = value;
}
@ -539,13 +541,13 @@ inline cvm::rvector operator * (cvm::rmatrix const &m,
/// Numerical recipes diagonalization
void jacobi (cvm::real **a, int n, cvm::real d[], cvm::real **v, int *nrot);
void jacobi (cvm::real **a, cvm::real d[], cvm::real **v, int *nrot);
/// Eigenvector sort
void eigsrt (cvm::real d[], cvm::real **v, int n);
void eigsrt (cvm::real d[], cvm::real **v);
/// Transpose the matrix
void transpose (cvm::real **v, int n);
void transpose (cvm::real **v);
@ -603,7 +605,7 @@ public:
}
/// \brief Set all components to a scalar
inline void set (cvm::real const value = 0.0)
inline void set (cvm::real const &value = 0.0)
{
q0 = q1 = q2 = q3 = value;
}
@ -645,7 +647,7 @@ public:
case 3:
return this->q3;
default:
cvm::fatal_error ("Error: incorrect quaternion component.\n");
cvm::error ("Error: incorrect quaternion component.\n");
return q0;
}
}
@ -662,9 +664,9 @@ public:
case 3:
return this->q3;
default:
cvm::fatal_error ("Error: trying to access a quaternion "
"component which is not between 0 and 3.\n");
return this->q0;
cvm::error ("Error: trying to access a quaternion "
"component which is not between 0 and 3.\n");
return 0.0;
}
}
@ -943,9 +945,9 @@ public:
/// Constructor after a quaternion
inline rotation (cvm::quaternion const &qi)
: b_debug_gradients (false)
: q (qi),
b_debug_gradients (false)
{
q = qi;
}
/// Constructor after an axis of rotation and an angle (in radians)
@ -1091,8 +1093,3 @@ protected:
#endif
// Emacs
// Local Variables:
// mode: C++
// End:

138
lib/colvars/colvarvalue.cpp
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#include <vector>
#include "colvarmodule.h"
@ -5,48 +7,60 @@
std::string const colvarvalue::type_desc[colvarvalue::type_quaternion+1] =
std::string const colvarvalue::type_desc[colvarvalue::type_all+1] =
{ "not_set",
"scalar number",
"3-dimensional vector",
"3-dimensional unit vector",
"4-dimensional unit vector" };
"3-dimensional tangent vector",
"4-dimensional unit quaternion",
"4-dimensional tangent vector",
};
size_t const colvarvalue::dof_num[ colvarvalue::type_quaternion+1] =
{ 0, 1, 3, 2, 3 };
std::string const colvarvalue::type_keyword[colvarvalue::type_all+1] =
{ "not_set",
"scalar",
"vector",
"unit_vector",
"",
"unit_quaternion",
"",
};
size_t const colvarvalue::dof_num[ colvarvalue::type_all+1] =
{ 0, 1, 3, 2, 2, 3, 3 };
void colvarvalue::undef_op() const
{
cvm::fatal_error ("Error: Undefined operation on a colvar of type \""+
colvarvalue::type_desc[this->value_type]+"\".\n");
cvm::error ("Error: Undefined operation on a colvar of type \""+
colvarvalue::type_desc[this->value_type]+"\".\n");
}
void colvarvalue::error_rside
(colvarvalue::Type const &vt) const
{
cvm::fatal_error ("Trying to assign a colvar value with type \""+
type_desc[this->value_type]+"\" to one with type \""+
type_desc[vt]+"\".\n");
cvm::error("Trying to assign a colvar value with type \""+
type_desc[this->value_type]+"\" to one with type \""+
type_desc[vt]+"\".\n");
}
void colvarvalue::error_lside
(colvarvalue::Type const &vt) const
void colvarvalue::error_lside(colvarvalue::Type const &vt) const
{
cvm::fatal_error ("Trying to use a colvar value with type \""+
type_desc[vt]+"\" as one of type \""+
type_desc[this->value_type]+"\".\n");
cvm::error("Trying to use a colvar value with type \""+
type_desc[vt]+"\" as one of type \""+
type_desc[this->value_type]+"\".\n");
}
void colvarvalue::inner_opt (colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner)
void colvarvalue::inner_opt(colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner)
{
// doing type check only once, here
colvarvalue::check_types (x, *xv);
colvarvalue::check_types(x, *xv);
std::vector<colvarvalue>::iterator &xvi = xv;
std::vector<cvm::real>::iterator &ii = inner;
@ -59,11 +73,13 @@ void colvarvalue::inner_opt (colvarvalue const &x,
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
while (xvi != xv_end) {
*(ii++) += (xvi++)->rvector_value * x.rvector_value;
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
while (xvi != xv_end) {
*(ii++) += ((xvi++)->quaternion_value).cosine (x.quaternion_value);
}
@ -73,13 +89,13 @@ void colvarvalue::inner_opt (colvarvalue const &x,
};
}
void colvarvalue::inner_opt (colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner)
void colvarvalue::inner_opt(colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner)
{
// doing type check only once, here
colvarvalue::check_types (x, *xv);
colvarvalue::check_types(x, *xv);
std::list<colvarvalue>::iterator &xvi = xv;
std::vector<cvm::real>::iterator &ii = inner;
@ -92,11 +108,13 @@ void colvarvalue::inner_opt (colvarvalue const &x,
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
while (xvi != xv_end) {
*(ii++) += (xvi++)->rvector_value * x.rvector_value;
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
while (xvi != xv_end) {
*(ii++) += ((xvi++)->quaternion_value).cosine (x.quaternion_value);
}
@ -107,21 +125,22 @@ void colvarvalue::inner_opt (colvarvalue const &x,
}
void colvarvalue::p2leg_opt (colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner)
void colvarvalue::p2leg_opt(colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner)
{
// doing type check only once, here
colvarvalue::check_types (x, *xv);
colvarvalue::check_types(x, *xv);
std::vector<colvarvalue>::iterator &xvi = xv;
std::vector<cvm::real>::iterator &ii = inner;
switch (x.value_type) {
case colvarvalue::type_scalar:
cvm::fatal_error ("Error: cannot calculate Legendre polynomials "
"for scalar variables.\n");
cvm::error("Error: cannot calculate Legendre polynomials "
"for scalar variables.\n");
return;
break;
case colvarvalue::type_vector:
while (xvi != xv_end) {
@ -133,12 +152,14 @@ void colvarvalue::p2leg_opt (colvarvalue const &x,
}
break;
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
while (xvi != xv_end) {
cvm::real const cosine = (xvi++)->rvector_value * x.rvector_value;
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
while (xvi != xv_end) {
cvm::real const cosine = (xvi++)->quaternion_value.cosine (x.quaternion_value);
*(ii++) += 1.5*cosine*cosine - 0.5;
@ -149,21 +170,21 @@ void colvarvalue::p2leg_opt (colvarvalue const &x,
};
}
void colvarvalue::p2leg_opt (colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner)
void colvarvalue::p2leg_opt(colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner)
{
// doing type check only once, here
colvarvalue::check_types (x, *xv);
colvarvalue::check_types(x, *xv);
std::list<colvarvalue>::iterator &xvi = xv;
std::vector<cvm::real>::iterator &ii = inner;
switch (x.value_type) {
case colvarvalue::type_scalar:
cvm::fatal_error ("Error: cannot calculate Legendre polynomials "
"for scalar variables.\n");
cvm::error("Error: cannot calculate Legendre polynomials "
"for scalar variables.\n");
break;
case colvarvalue::type_vector:
while (xvi != xv_end) {
@ -175,12 +196,14 @@ void colvarvalue::p2leg_opt (colvarvalue const &x,
}
break;
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
while (xvi != xv_end) {
cvm::real const cosine = (xvi++)->rvector_value * x.rvector_value;
*(ii++) += 1.5*cosine*cosine - 0.5;
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
while (xvi != xv_end) {
cvm::real const cosine = (xvi++)->quaternion_value.cosine (x.quaternion_value);
*(ii++) += 1.5*cosine*cosine - 0.5;
@ -196,12 +219,17 @@ std::ostream & operator << (std::ostream &os, colvarvalue const &x)
{
switch (x.type()) {
case colvarvalue::type_scalar:
os << x.real_value; break;
os << x.real_value;
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
os << x.rvector_value; break;
case colvarvalue::type_unitvectorderiv:
os << x.rvector_value;
break;
case colvarvalue::type_quaternion:
os << x.quaternion_value; break;
case colvarvalue::type_quaternionderiv:
os << x.quaternion_value;
break;
case colvarvalue::type_notset:
os << "not set"; break;
}
@ -211,7 +239,9 @@ std::ostream & operator << (std::ostream &os, colvarvalue const &x)
std::ostream & operator << (std::ostream &os, std::vector<colvarvalue> const &v)
{
for (size_t i = 0; i < v.size(); i++) os << v[i];
for (size_t i = 0; i < v.size(); i++) {
os << v[i];
}
return os;
}
@ -219,8 +249,9 @@ std::ostream & operator << (std::ostream &os, std::vector<colvarvalue> const &v)
std::istream & operator >> (std::istream &is, colvarvalue &x)
{
if (x.type() == colvarvalue::type_notset) {
cvm::fatal_error ("Trying to read from a stream a colvarvalue, "
"which has not yet been assigned a data type.\n");
cvm::error("Trying to read from a stream a colvarvalue, "
"which has not yet been assigned a data type.\n");
return is;
}
switch (x.type()) {
@ -228,30 +259,39 @@ std::istream & operator >> (std::istream &is, colvarvalue &x)
is >> x.real_value;
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
is >> x.rvector_value;
break;
case colvarvalue::type_unitvector:
is >> x.rvector_value;
x.apply_constraints();
break;
case colvarvalue::type_quaternion:
is >> x.quaternion_value;
x.apply_constraints();
break;
case colvarvalue::type_quaternionderiv:
is >> x.quaternion_value;
break;
default:
x.undef_op();
}
x.apply_constraints();
return is;
}
size_t colvarvalue::output_width (size_t const &real_width) const
size_t colvarvalue::output_width(size_t const &real_width) const
{
switch (this->value_type) {
case colvarvalue::type_scalar:
return real_width;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
return cvm::rvector::output_width (real_width);
case colvarvalue::type_unitvectorderiv:
return cvm::rvector::output_width(real_width);
case colvarvalue::type_quaternion:
return cvm::quaternion::output_width (real_width);
case colvarvalue::type_quaternionderiv:
return cvm::quaternion::output_width(real_width);
case colvarvalue::type_notset:
default:
return 0;

370
lib/colvars/colvarvalue.h
View File

@ -1,3 +1,5 @@
/// -*- c++ -*-
#ifndef COLVARVALUE_H
#define COLVARVALUE_H
@ -72,15 +74,22 @@ public:
type_vector,
/// 3-dimensional unit vector, implemented as \link colvarmodule::rvector \endlink
type_unitvector,
/// 3-dimensional vector that is a derivative of a unitvector
type_unitvectorderiv,
/// 4-dimensional unit vector representing a rotation, implemented as \link colvarmodule::quaternion \endlink
type_quaternion
type_quaternion,
/// 4-dimensional vector that is a derivative of a quaternion
type_quaternionderiv,
/// bogus type to hold the size of the enum
type_all
};
/// Runtime description of value types
std::string static const type_desc[colvarvalue::type_quaternion+1];
std::string static const type_desc[colvarvalue::type_all+1];
/// User keywords for specifying value types
std::string static const type_keyword[colvarvalue::type_all+1];
/// Number of degrees of freedom for each type
size_t static const dof_num[ colvarvalue::type_quaternion+1];
size_t static const dof_num[ colvarvalue::type_all+1];
/// \brief Real data member
cvm::real real_value;
@ -102,43 +111,43 @@ public:
/// \brief Default constructor: this class defaults to a scalar
/// number and always behaves like it unless you change its type
inline colvarvalue()
: real_value (0.0), value_type (type_scalar)
: real_value(0.0), value_type(type_scalar)
{}
/// Constructor from a type specification
inline colvarvalue (Type const &vti)
: value_type (vti)
inline colvarvalue(Type const &vti)
: value_type(vti)
{
reset();
}
/// Copy constructor from real base type
inline colvarvalue (cvm::real const &x)
: real_value (x), value_type (type_scalar)
inline colvarvalue(cvm::real const &x)
: real_value(x), value_type(type_scalar)
{}
/// \brief Copy constructor from rvector base type (Note: this sets
/// automatically a type \link type_vector \endlink , if you want a
/// \link type_unitvector \endlink you must set it explicitly)
inline colvarvalue (cvm::rvector const &v)
: rvector_value (v), value_type (type_vector)
inline colvarvalue(cvm::rvector const &v)
: rvector_value(v), value_type(type_vector)
{}
/// \brief Copy constructor from rvector base type (additional
/// argument to make possible to choose a \link type_unitvector
/// \endlink
inline colvarvalue (cvm::rvector const &v, Type const &vti)
: rvector_value (v), value_type (vti)
inline colvarvalue(cvm::rvector const &v, Type const &vti)
: rvector_value(v), value_type(vti)
{}
/// \brief Copy constructor from quaternion base type
inline colvarvalue (cvm::quaternion const &q)
: quaternion_value (q), value_type (type_quaternion)
inline colvarvalue(cvm::quaternion const &q)
: quaternion_value(q), value_type(type_quaternion)
{}
/// Copy constructor from another \link colvarvalue \endlink
inline colvarvalue (colvarvalue const &x)
: value_type (x.value_type)
inline colvarvalue(colvarvalue const &x)
: value_type(x.value_type)
{
reset();
@ -160,18 +169,15 @@ public:
}
/// Set to the null value for the data type currently defined
void reset();
/// \brief If the variable has constraints (e.g. unitvector or
/// quaternion), transform it to satisfy them; use it when the \link
/// colvarvalue \endlink is not calculated from \link cvc
/// \endlink objects, but manipulated by you
/// quaternion), transform it to satisfy them; this function needs
/// to be called only when the \link colvarvalue \endlink
/// is calculated outside of \link cvc \endlink objects
void apply_constraints();
/// Get the current type
inline Type type() const
{
@ -179,7 +185,7 @@ public:
}
/// Set the type explicitly
inline void type (Type const &vti)
inline void type(Type const &vti)
{
reset();
value_type = vti;
@ -187,20 +193,24 @@ public:
}
/// Set the type after another \link colvarvalue \endlink
inline void type (colvarvalue const &x)
inline void type(colvarvalue const &x)
{
reset();
value_type = x.value_type;
reset();
}
/// Make the type a derivative of the original type
/// (constraints do not apply on time derivatives of vector values)
inline void is_derivative();
/// Square norm of this colvarvalue
cvm::real norm2() const;
/// Norm of this colvarvalue
inline cvm::real norm() const
{
return std::sqrt (this->norm2());
return std::sqrt(this->norm2());
}
/// \brief Return the value whose scalar product with this value is
@ -208,10 +218,10 @@ public:
inline colvarvalue inverse() const;
/// Square distance between this \link colvarvalue \endlink and another
cvm::real dist2 (colvarvalue const &x2) const;
cvm::real dist2(colvarvalue const &x2) const;
/// Derivative with respect to this \link colvarvalue \endlink of the square distance
colvarvalue dist2_grad (colvarvalue const &x2) const;
colvarvalue dist2_grad(colvarvalue const &x2) const;
/// Assignment operator (type of x is checked)
colvarvalue & operator = (colvarvalue const &x);
@ -225,50 +235,57 @@ public:
// Casting operator
inline operator cvm::real() const
{
if (value_type != type_scalar) error_rside (type_scalar);
if (value_type != type_scalar) {
error_rside(type_scalar);
}
return real_value;
}
// Casting operator
inline operator cvm::rvector() const
{
if ( (value_type != type_vector) && (value_type != type_unitvector))
error_rside (type_vector);
if ((value_type != type_vector) &&
(value_type != type_unitvector) &&
(value_type != type_unitvectorderiv)) {
error_rside(type_vector);
}
return rvector_value;
}
// Casting operator
inline operator cvm::quaternion() const
{
if (value_type != type_quaternion) error_rside (type_quaternion);
if ((value_type != type_quaternion) &&
(value_type != type_quaternionderiv)) {
error_rside(type_quaternion);
}
return quaternion_value;
}
/// Special case when the variable is a real number, and all operations are defined
inline bool is_scalar()
inline bool is_scalar() const
{
return (value_type == type_scalar);
}
/// Ensure that the two types are the same within a binary operator
void static check_types (colvarvalue const &x1, colvarvalue const &x2);
void static check_types(colvarvalue const &x1, colvarvalue const &x2);
/// Undefined operation
void undef_op() const;
/// Trying to assign this \link colvarvalue \endlink object to
/// another object set with a different type
void error_lside (Type const &vt) const;
void error_lside(Type const &vt) const;
/// Trying to assign another \link colvarvalue \endlink object set
/// with a different type to this object
void error_rside (Type const &vt) const;
void error_rside(Type const &vt) const;
/// Give the number of characters required to output this
/// colvarvalue, given the current type assigned and the number of
/// characters for a real number
size_t output_width (size_t const &real_width) const;
size_t output_width(size_t const &real_width) const;
// optimized routines for operations with an array; xv and inner as
@ -277,32 +294,32 @@ public:
/// \brief Optimized routine for the inner product of one collective
/// variable with an array
void static inner_opt (colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner);
void static inner_opt(colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner);
/// \brief Optimized routine for the inner product of one collective
/// variable with an array
void static inner_opt (colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner);
void static inner_opt(colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner);
/// \brief Optimized routine for the second order Legendre
/// polynomial, (3cos^2(w)-1)/2, of one collective variable with an
/// array
void static p2leg_opt (colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner);
void static p2leg_opt(colvarvalue const &x,
std::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner);
/// \brief Optimized routine for the second order Legendre
/// polynomial of one collective variable with an array
void static p2leg_opt (colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner);
void static p2leg_opt(colvarvalue const &x,
std::list<colvarvalue>::iterator &xv,
std::list<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &inner);
};
@ -312,14 +329,16 @@ inline void colvarvalue::reset()
{
switch (value_type) {
case colvarvalue::type_scalar:
real_value = cvm::real (0.0);
real_value = cvm::real(0.0);
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
rvector_value = cvm::rvector (0.0, 0.0, 0.0);
case colvarvalue::type_unitvectorderiv:
rvector_value = cvm::rvector(0.0, 0.0, 0.0);
break;
case colvarvalue::type_quaternion:
quaternion_value = cvm::quaternion (0.0, 0.0, 0.0, 0.0);
case colvarvalue::type_quaternionderiv:
quaternion_value = cvm::quaternion(0.0, 0.0, 0.0, 0.0);
break;
case colvarvalue::type_notset:
default:
@ -332,14 +351,36 @@ inline void colvarvalue::apply_constraints()
{
switch (value_type) {
case colvarvalue::type_scalar:
break;
case colvarvalue::type_vector:
break;
case colvarvalue::type_unitvectorderiv:
case colvarvalue::type_quaternionderiv:
break;
case colvarvalue::type_unitvector:
rvector_value /= std::sqrt (rvector_value.norm2());
rvector_value /= std::sqrt(rvector_value.norm2());
break;
case colvarvalue::type_quaternion:
quaternion_value /= std::sqrt (quaternion_value.norm2());
quaternion_value /= std::sqrt(quaternion_value.norm2());
break;
case colvarvalue::type_notset:
default:
break;
}
}
inline void colvarvalue::is_derivative()
{
switch (value_type) {
case colvarvalue::type_scalar:
case colvarvalue::type_vector:
case colvarvalue::type_unitvectorderiv:
case colvarvalue::type_quaternionderiv:
break;
case colvarvalue::type_unitvector:
type(colvarvalue::type_unitvectorderiv);
break;
case colvarvalue::type_quaternion:
type(colvarvalue::type_quaternionderiv);
break;
case colvarvalue::type_notset:
default:
@ -356,8 +397,10 @@ inline cvm::real colvarvalue::norm2() const
return (this->real_value)*(this->real_value);
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
return (this->rvector_value).norm2();
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return (this->quaternion_value).norm2();
case colvarvalue::type_notset:
default:
@ -370,16 +413,19 @@ inline colvarvalue colvarvalue::inverse() const
{
switch (value_type) {
case colvarvalue::type_scalar:
return colvarvalue (1.0/real_value);
return colvarvalue(1.0/real_value);
case colvarvalue::type_vector:
return colvarvalue (cvm::rvector (1.0/rvector_value.x,
1.0/rvector_value.y,
1.0/rvector_value.z));
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
return colvarvalue(cvm::rvector(1.0/rvector_value.x,
1.0/rvector_value.y,
1.0/rvector_value.z));
case colvarvalue::type_quaternion:
return colvarvalue (cvm::quaternion (1.0/quaternion_value.q0,
1.0/quaternion_value.q1,
1.0/quaternion_value.q2,
1.0/quaternion_value.q3));
case colvarvalue::type_quaternionderiv:
return colvarvalue(cvm::quaternion(1.0/quaternion_value.q0,
1.0/quaternion_value.q1,
1.0/quaternion_value.q2,
1.0/quaternion_value.q3));
case colvarvalue::type_notset:
default:
undef_op();
@ -387,12 +433,11 @@ inline colvarvalue colvarvalue::inverse() const
return colvarvalue();
}
inline colvarvalue & colvarvalue::operator = (colvarvalue const &x)
{
if (this->value_type != type_notset)
if (this->value_type != x.value_type)
error_lside (x.value_type);
error_lside(x.value_type);
this->value_type = x.value_type;
@ -402,9 +447,11 @@ inline colvarvalue & colvarvalue::operator = (colvarvalue const &x)
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
this->rvector_value = x.rvector_value;
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
this->quaternion_value = x.quaternion_value;
break;
case colvarvalue::type_notset:
@ -418,7 +465,7 @@ inline colvarvalue & colvarvalue::operator = (colvarvalue const &x)
inline void colvarvalue::operator += (colvarvalue const &x)
{
if (colvarvalue::type_checking())
colvarvalue::check_types (*this, x);
colvarvalue::check_types(*this, x);
switch (this->value_type) {
case colvarvalue::type_scalar:
@ -426,9 +473,11 @@ inline void colvarvalue::operator += (colvarvalue const &x)
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
this->rvector_value += x.rvector_value;
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
this->quaternion_value += x.quaternion_value;
break;
case colvarvalue::type_notset:
@ -440,16 +489,21 @@ inline void colvarvalue::operator += (colvarvalue const &x)
inline void colvarvalue::operator -= (colvarvalue const &x)
{
if (colvarvalue::type_checking())
colvarvalue::check_types (*this, x);
colvarvalue::check_types(*this, x);
switch (value_type) {
case colvarvalue::type_scalar:
real_value -= x.real_value; break;
real_value -= x.real_value;
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
rvector_value -= x.rvector_value; break;
case colvarvalue::type_unitvectorderiv:
rvector_value -= x.rvector_value;
break;
case colvarvalue::type_quaternion:
quaternion_value -= x.quaternion_value; break;
case colvarvalue::type_quaternionderiv:
quaternion_value -= x.quaternion_value;
break;
case colvarvalue::type_notset:
default:
undef_op();
@ -463,10 +517,11 @@ inline void colvarvalue::operator *= (cvm::real const &a)
real_value *= a;
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
rvector_value *= a;
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
quaternion_value *= a;
break;
case colvarvalue::type_notset:
@ -482,8 +537,10 @@ inline void colvarvalue::operator /= (cvm::real const &a)
real_value /= a; break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
rvector_value /= a; break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
quaternion_value /= a; break;
case colvarvalue::type_notset:
default:
@ -498,22 +555,24 @@ inline colvarvalue operator + (colvarvalue const &x1,
colvarvalue const &x2)
{
if (colvarvalue::type_checking())
colvarvalue::check_types (x1, x2);
colvarvalue::check_types(x1, x2);
switch (x1.value_type) {
case colvarvalue::type_scalar:
return colvarvalue (x1.real_value + x2.real_value);
return colvarvalue(x1.real_value + x2.real_value);
case colvarvalue::type_vector:
return colvarvalue (x1.rvector_value + x2.rvector_value);
return colvarvalue(x1.rvector_value + x2.rvector_value);
case colvarvalue::type_unitvector:
return colvarvalue (x1.rvector_value + x2.rvector_value,
colvarvalue::type_unitvector);
case colvarvalue::type_unitvectorderiv:
return colvarvalue(x1.rvector_value + x2.rvector_value,
colvarvalue::type_unitvector);
case colvarvalue::type_quaternion:
return colvarvalue (x1.quaternion_value + x2.quaternion_value);
case colvarvalue::type_quaternionderiv:
return colvarvalue(x1.quaternion_value + x2.quaternion_value);
case colvarvalue::type_notset:
default:
x1.undef_op();
return colvarvalue (colvarvalue::type_notset);
return colvarvalue(colvarvalue::type_notset);
};
}
@ -521,21 +580,23 @@ inline colvarvalue operator - (colvarvalue const &x1,
colvarvalue const &x2)
{
if (colvarvalue::type_checking())
colvarvalue::check_types (x1, x2);
colvarvalue::check_types(x1, x2);
switch (x1.value_type) {
case colvarvalue::type_scalar:
return colvarvalue (x1.real_value - x2.real_value);
return colvarvalue(x1.real_value - x2.real_value);
case colvarvalue::type_vector:
return colvarvalue (x1.rvector_value - x2.rvector_value);
return colvarvalue(x1.rvector_value - x2.rvector_value);
case colvarvalue::type_unitvector:
return colvarvalue (x1.rvector_value - x2.rvector_value,
colvarvalue::type_unitvector);
case colvarvalue::type_unitvectorderiv:
return colvarvalue(x1.rvector_value - x2.rvector_value,
colvarvalue::type_unitvector);
case colvarvalue::type_quaternion:
return colvarvalue (x1.quaternion_value - x2.quaternion_value);
case colvarvalue::type_quaternionderiv:
return colvarvalue(x1.quaternion_value - x2.quaternion_value);
default:
x1.undef_op();
return colvarvalue (colvarvalue::type_notset);
return colvarvalue(colvarvalue::type_notset);
};
}
@ -547,18 +608,20 @@ inline colvarvalue operator * (cvm::real const &a,
{
switch (x.value_type) {
case colvarvalue::type_scalar:
return colvarvalue (a * x.real_value);
return colvarvalue(a * x.real_value);
case colvarvalue::type_vector:
return colvarvalue (a * x.rvector_value);
return colvarvalue(a * x.rvector_value);
case colvarvalue::type_unitvector:
return colvarvalue (a * x.rvector_value,
colvarvalue::type_unitvector);
case colvarvalue::type_unitvectorderiv:
return colvarvalue(a * x.rvector_value,
colvarvalue::type_unitvector);
case colvarvalue::type_quaternion:
return colvarvalue (a * x.quaternion_value);
case colvarvalue::type_quaternionderiv:
return colvarvalue(a * x.quaternion_value);
case colvarvalue::type_notset:
default:
x.undef_op();
return colvarvalue (colvarvalue::type_notset);
return colvarvalue(colvarvalue::type_notset);
}
}
@ -567,18 +630,20 @@ inline colvarvalue operator * (colvarvalue const &x,
{
switch (x.value_type) {
case colvarvalue::type_scalar:
return colvarvalue (x.real_value * a);
return colvarvalue(x.real_value * a);
case colvarvalue::type_vector:
return colvarvalue (x.rvector_value * a);
return colvarvalue(x.rvector_value * a);
case colvarvalue::type_unitvector:
return colvarvalue (x.rvector_value * a,
colvarvalue::type_unitvector);
case colvarvalue::type_unitvectorderiv:
return colvarvalue(x.rvector_value * a,
colvarvalue::type_unitvector);
case colvarvalue::type_quaternion:
return colvarvalue (x.quaternion_value * a);
case colvarvalue::type_quaternionderiv:
return colvarvalue(x.quaternion_value * a);
case colvarvalue::type_notset:
default:
x.undef_op();
return colvarvalue (colvarvalue::type_notset);
return colvarvalue(colvarvalue::type_notset);
}
}
@ -587,18 +652,20 @@ inline colvarvalue operator / (colvarvalue const &x,
{
switch (x.value_type) {
case colvarvalue::type_scalar:
return colvarvalue (x.real_value / a);
return colvarvalue(x.real_value / a);
case colvarvalue::type_vector:
return colvarvalue (x.rvector_value / a);
return colvarvalue(x.rvector_value / a);
case colvarvalue::type_unitvector:
return colvarvalue (x.rvector_value / a,
colvarvalue::type_unitvector);
case colvarvalue::type_unitvectorderiv:
return colvarvalue(x.rvector_value / a,
colvarvalue::type_unitvector);
case colvarvalue::type_quaternion:
return colvarvalue (x.quaternion_value / a);
case colvarvalue::type_quaternionderiv:
return colvarvalue(x.quaternion_value / a);
case colvarvalue::type_notset:
default:
x.undef_op();
return colvarvalue (colvarvalue::type_notset);
return colvarvalue(colvarvalue::type_notset);
}
}
@ -609,18 +676,20 @@ inline cvm::real operator * (colvarvalue const &x1,
colvarvalue const &x2)
{
if (colvarvalue::type_checking())
colvarvalue::check_types (x1, x2);
colvarvalue::check_types(x1, x2);
switch (x1.value_type) {
case colvarvalue::type_scalar:
return (x1.real_value * x2.real_value);
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
return (x1.rvector_value * x2.rvector_value);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
// the "*" product is the quaternion product, here the inner
// member function is used instead
return (x1.quaternion_value.inner (x2.quaternion_value));
return (x1.quaternion_value.inner(x2.quaternion_value));
case colvarvalue::type_notset:
default:
x1.undef_op();
@ -630,10 +699,10 @@ inline cvm::real operator * (colvarvalue const &x1,
inline cvm::real colvarvalue::dist2 (colvarvalue const &x2) const
inline cvm::real colvarvalue::dist2(colvarvalue const &x2) const
{
if (colvarvalue::type_checking())
colvarvalue::check_types (*this, x2);
colvarvalue::check_types(*this, x2);
switch (this->value_type) {
case colvarvalue::type_scalar:
@ -641,12 +710,14 @@ inline cvm::real colvarvalue::dist2 (colvarvalue const &x2) const
case colvarvalue::type_vector:
return (this->rvector_value - x2.rvector_value).norm2();
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
// angle between (*this) and x2 is the distance
return std::acos (this->rvector_value * x2.rvector_value) * std::acos (this->rvector_value * x2.rvector_value);
return std::acos(this->rvector_value * x2.rvector_value) * std::acos(this->rvector_value * x2.rvector_value);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
// angle between (*this) and x2 is the distance, the quaternion
// object has it implemented internally
return this->quaternion_value.dist2 (x2.quaternion_value);
return this->quaternion_value.dist2(x2.quaternion_value);
case colvarvalue::type_notset:
default:
this->undef_op();
@ -655,10 +726,10 @@ inline cvm::real colvarvalue::dist2 (colvarvalue const &x2) const
}
inline colvarvalue colvarvalue::dist2_grad (colvarvalue const &x2) const
inline colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const
{
if (colvarvalue::type_checking())
colvarvalue::check_types (*this, x2);
colvarvalue::check_types(*this, x2);
switch (this->value_type) {
case colvarvalue::type_scalar:
@ -666,62 +737,61 @@ inline colvarvalue colvarvalue::dist2_grad (colvarvalue const &x2) const
case colvarvalue::type_vector:
return 2.0 * (this->rvector_value - x2.rvector_value);
case colvarvalue::type_unitvector:
case colvarvalue::type_unitvectorderiv:
{
cvm::rvector const &v1 = this->rvector_value;
cvm::rvector const &v2 = x2.rvector_value;
cvm::real const cos_t = v1 * v2;
cvm::real const sin_t = std::sqrt (1.0 - cos_t*cos_t);
return colvarvalue ( 2.0 * sin_t *
cvm::rvector ( (-1.0) * sin_t * v2.x +
cos_t/sin_t * (v1.x - cos_t*v2.x),
(-1.0) * sin_t * v2.y +
cos_t/sin_t * (v1.y - cos_t*v2.y),
(-1.0) * sin_t * v2.z +
cos_t/sin_t * (v1.z - cos_t*v2.z)
),
colvarvalue::type_unitvector );
cvm::real const sin_t = std::sqrt(1.0 - cos_t*cos_t);
return colvarvalue( 2.0 * sin_t *
cvm::rvector((-1.0) * sin_t * v2.x +
cos_t/sin_t * (v1.x - cos_t*v2.x),
(-1.0) * sin_t * v2.y +
cos_t/sin_t * (v1.y - cos_t*v2.y),
(-1.0) * sin_t * v2.z +
cos_t/sin_t * (v1.z - cos_t*v2.z)
),
colvarvalue::type_unitvector );
}
case colvarvalue::type_quaternion:
return this->quaternion_value.dist2_grad (x2.quaternion_value);
case colvarvalue::type_quaternionderiv:
return this->quaternion_value.dist2_grad(x2.quaternion_value);
case colvarvalue::type_notset:
default:
this->undef_op();
return colvarvalue (colvarvalue::type_notset);
return colvarvalue(colvarvalue::type_notset);
};
}
inline void colvarvalue::check_types (colvarvalue const &x1,
colvarvalue const &x2)
inline void colvarvalue::check_types(colvarvalue const &x1,
colvarvalue const &x2)
{
if (x1.value_type != x2.value_type) {
cvm::log ("x1 type = "+cvm::to_str (x1.value_type)+
", x2 type = "+cvm::to_str (x2.value_type)+"\n");
cvm::fatal_error ("Performing an operation between two colvar "
"values with different types, \""+
colvarvalue::type_desc[x1.value_type]+
"\" and \""+
colvarvalue::type_desc[x2.value_type]+
"\".\n");
if (((x1.value_type == type_unitvector) &&
(x2.value_type == type_unitvectorderiv)) ||
((x2.value_type == type_unitvector) &&
(x1.value_type == type_unitvectorderiv)) ||
((x1.value_type == type_quaternion) &&
(x2.value_type == type_quaternionderiv)) ||
((x2.value_type == type_quaternion) &&
(x1.value_type == type_quaternionderiv))) {
return;
}
cvm::error("Performing an operation between two colvar "
"values with different types, \""+
colvarvalue::type_desc[x1.value_type]+
"\" and \""+
colvarvalue::type_desc[x2.value_type]+
"\".\n");
}
}
std::ostream & operator << (std::ostream &os, colvarvalue const &x);
std::ostream & operator << (std::ostream &os, std::vector<colvarvalue> const &v);
std::istream & operator >> (std::istream &is, colvarvalue &x);
#endif
// Emacs
// Local Variables:
// mode: C++
// End: