mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10118 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
38112d0063
commit
4da20dce99
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@ -1,4 +1,4 @@
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# library build makefile for colvars module
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# library build -*- makefile -*- for colvars module
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# which file will be copied to Makefile.lammps
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@ -25,11 +25,13 @@ EXE = #colvars_standalone
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# ------ MAKE PROCEDURE ------
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default: $(LIB) $(EXE)
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default: $(LIB) $(EXE) Makefile.lammps
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Makefile.lammps:
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@cp $(EXTRAMAKE) Makefile.lammps
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$(LIB): $(OBJ)
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$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
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@cp $(EXTRAMAKE) Makefile.lammps
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colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
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$(CXX) -o $@ $(CXXFLAGS) $^
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@ -1,4 +1,4 @@
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# library build makefile for colvars module
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# library build -*- makefile -*- for colvars module
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# which file will be copied to Makefile.lammps
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@ -6,12 +6,12 @@ EXTRAMAKE = Makefile.lammps.empty
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# ------ SETTINGS ------
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CXX = i686-pc-mingw32-g++
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CXX = i686-w64-mingw32-g++
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CXXFLAGS = -O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
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-fno-rtti -fno-exceptions -finline-functions \
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-ffast-math -funroll-loops -fstrict-aliasing \
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-Wall -W -Wno-uninitialized
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ARCHIVE = i686-pc-mingw32-ar
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ARCHIVE = i686-w64-mingw32-ar
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ARCHFLAG = -rscv
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SHELL = /bin/sh
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@ -22,19 +22,26 @@ SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias.cpp colvarbias_meta.cpp \
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colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp \
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colvargrid.cpp colvarmodule.cpp colvarparse.cpp colvarvalue.cpp
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LIB = libcolvars.a
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OBJ = $(SRC:.cpp=.o)
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DIR = Obj_mingw32/
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LIB = $(DIR)libcolvars.a
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OBJ = $(SRC:%.cpp=$(DIR)%.o)
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EXE = #colvars_standalone
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# ------ MAKE PROCEDURE ------
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default: $(LIB) $(EXE)
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default: $(DIR) $(LIB) $(EXE) Makefile.lammps
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$(LIB): $(OBJ)
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$(DIR):
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mkdir $(DIR)
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Makefile.lammps:
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@cp $(EXTRAMAKE) Makefile.lammps
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$(LIB): $(DIR) $(OBJ)
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$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
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@cp $(EXTRAMAKE) Makefile.lammps
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colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
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$(DIR)colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
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$(CXX) -o $@ $(CXXFLAGS) $^
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# ------ MAKE FLAGS ------
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@ -46,58 +53,59 @@ colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
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# ------ COMPILE RULES ------
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.cpp.o:
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$(CXX) $(CXXFLAGS) -c $<
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$(DIR)%.o: %.cpp
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$(CXX) $(CXXFLAGS) -c $< -o $@
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# ------ DEPENDENCIES ------
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#
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colvars_main.o: colvars_main.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvars_main.o: colvars_main.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarproxy_standalone.h colvaratoms.h colvarparse.h colvarvalue.h
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colvarproxy_standalone.o: colvarproxy_standalone.cpp colvarmodule.h \
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$(DIR)colvarproxy_standalone.o: colvarproxy_standalone.cpp colvarmodule.h \
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colvartypes.h colvarproxy.h colvaratoms.h colvarparse.h colvarvalue.h \
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colvarproxy_standalone.h
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colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarparse.h colvarvalue.h colvaratoms.h
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colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
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$(DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
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colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
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colvarbias.h colvargrid.h
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colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarvalue.h colvarbias.h colvar.h colvarparse.h
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colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
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$(DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
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colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
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colvarbias_meta.h colvarbias.h colvargrid.h
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colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h
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colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
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$(DIR)colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
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colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
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colvaratoms.h
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colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
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colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
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$(DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
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colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
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colvar.h colvarcomp.h
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colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
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$(DIR)colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
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colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
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colvarcomp.h colvaratoms.h
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colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
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$(DIR)colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
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colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarcomp.h \
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colvaratoms.h
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colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
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$(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
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colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
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colvarcomp.h colvaratoms.h
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colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
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colvargrid.h
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colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarparse.h colvarvalue.h colvar.h colvarbias.h colvarbias_meta.h \
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colvargrid.h colvarbias_abf.h
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colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarvalue.h colvarparse.h
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colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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$(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
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colvarvalue.h
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# ------ CLEAN ------
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clean:
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-rm *.o *~ $(LIB)
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-rm $(DIR)*.o *~ $(LIB)
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-rmdir $(DIR)
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@ -4,9 +4,24 @@ that allows enhanced sampling in molecular dynamics simulations.
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The module is written to maximize performance, portability,
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flexibility of usage for the user, and extensibility for the developer.
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The following publication describes the principles of
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The development of the colvars library is now hosted on github at:
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http://colvars.github.io/
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You can use this site to get access to the latest development sources
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and the up-to-date documentation.
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Copy of the specific documentation is also in
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doc/PDF/colvars-refman-lammps.pdf
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Please report bugs and request new features at:
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https://github.com/colvars/colvars/issues
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The following publications describe the principles of
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the implementation of this library:
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Using collective variables to drive molecular dynamics simulations,
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Giacomo Fiorin , Michael L. Klein & Jérôme Hénin (2013):
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Molecular Physics DOI:10.1080/00268976.2013.813594
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Exploring Multidimensional Free Energy Landscapes Using
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Time-Dependent Biases on Collective Variables,
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J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein,
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@ -167,6 +167,9 @@ colvar::colvar (std::string const &conf)
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// check the available features of each cvc
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for (size_t i = 0; i < cvcs.size(); i++) {
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if ((cvcs[i])->b_debug_gradients)
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enable (task_gradients);
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if ((cvcs[i])->sup_np != 1) {
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if (cvm::debug() && b_linear)
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cvm::log ("Warning: You are using a non-linear polynomial "
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@ -664,6 +667,18 @@ void colvar::disable (colvar::task const &t)
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}
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void colvar::setup() {
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// loop over all components to reset masses of all groups
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for (size_t i = 0; i < cvcs.size(); i++) {
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for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
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cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
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atoms.read_positions();
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atoms.reset_mass(name,i,ig);
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}
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}
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}
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colvar::~colvar()
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{
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for (size_t i = 0; i < cvcs.size(); i++) {
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@ -682,6 +697,8 @@ void colvar::calc()
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cvm::log ("Calculating colvar \""+this->name+"\".\n");
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// prepare atom groups for calculation
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if (cvm::debug())
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cvm::log ("Collecting data from atom groups.\n");
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for (size_t i = 0; i < cvcs.size(); i++) {
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for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
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cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
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@ -710,6 +727,8 @@ void colvar::calc()
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// calculate the value of the colvar
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if (cvm::debug())
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cvm::log ("Calculating colvar components.\n");
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x.reset();
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if (x.type() == colvarvalue::type_scalar) {
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// polynomial combination allowed
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@ -288,6 +288,9 @@ public:
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/// Disable the specified task
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void disable (colvar::task const &t);
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/// Get ready for a run and possibly re-initialize internal data
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void setup();
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/// Destructor
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~colvar();
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@ -71,6 +71,18 @@ void cvm::atom_group::add_atom (cvm::atom const &a)
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}
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void cvm::atom_group::reset_mass(std::string &name, int i, int j)
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{
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total_mass = 0.0;
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for (cvm::atom_iter ai = this->begin();
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ai != this->end(); ai++) {
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total_mass += ai->mass;
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}
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cvm::log ("Re-initialized atom group "+name+":"+cvm::to_str (i)+"/"+
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cvm::to_str (j)+". "+ cvm::to_str (this->size())+
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" atoms: total mass = "+cvm::to_str (this->total_mass)+".\n");
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}
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void cvm::atom_group::parse (std::string const &conf,
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char const *key)
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{
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@ -129,6 +141,25 @@ void cvm::atom_group::parse (std::string const &conf,
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atom_indexes.clear();
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}
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std::string index_group_name;
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if (get_keyval (group_conf, "indexGroup", index_group_name)) {
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// use an index group from the index file read globally
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std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
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std::list<std::vector<int> >::iterator index_groups_i = cvm::index_groups.begin();
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for ( ; names_i != cvm::index_group_names.end() ; names_i++, index_groups_i++) {
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if (*names_i == index_group_name)
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break;
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}
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if (names_i == cvm::index_group_names.end()) {
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cvm::fatal_error ("Error: could not find index group "+
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index_group_name+" among those provided by the index file.\n");
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}
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this->reserve (index_groups_i->size());
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for (size_t i = 0; i < index_groups_i->size(); i++) {
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this->push_back (cvm::atom ((*index_groups_i)[i]));
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}
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}
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||||
}
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||||
|
||||
{
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@ -23,7 +23,7 @@ protected:
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/// \brief Index in the list of atoms involved by the colvars (\b
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/// NOT in the global topology!)
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size_t index;
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int index;
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public:
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@ -57,8 +57,8 @@ public:
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/// implementation
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cvm::rvector grad;
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/// \brief Default constructor, setting id to a non-valid value
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inline atom() {}
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/// \brief Default constructor, setting id and index to invalid numbers
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atom() : id (-1), index (-1) { reset_data(); }
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/// \brief Initialize an atom for collective variable calculation
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/// and get its internal identifier \param atom_number Atom index in
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||||
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|
@ -121,7 +121,7 @@ class colvarmodule::atom_group
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public colvarparse
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||||
{
|
||||
public:
|
||||
// Note: all members here are kept public, to make possible to any
|
||||
// Note: all members here are kept public, to allow any
|
||||
// object accessing and manipulating them
|
||||
|
||||
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||||
|
|
@ -202,6 +202,11 @@ public:
|
|||
/// \brief Add an atom to this group
|
||||
void add_atom (cvm::atom const &a);
|
||||
|
||||
/// \brief Re-initialize the total mass of a group.
|
||||
/// This is needed in case the hosting MD code has an option to
|
||||
/// change atom masses after their initialization.
|
||||
void reset_mass (std::string &name, int i, int j);
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||||
|
||||
/// \brief Default constructor
|
||||
atom_group();
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||||
|
||||
|
|
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|||
|
|
@ -41,10 +41,11 @@ colvarbias::colvarbias (std::string const &conf, char const *key)
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add_colvar (colvars_str[i]);
|
||||
}
|
||||
}
|
||||
|
||||
if (!colvars.size()) {
|
||||
cvm::fatal_error ("Error: no collective variables specified.\n");
|
||||
}
|
||||
|
||||
get_keyval (conf, "outputEnergy", b_output_energy, false);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -82,6 +83,40 @@ void colvarbias::communicate_forces()
|
|||
}
|
||||
|
||||
|
||||
void colvarbias::change_configuration(std::string const &conf)
|
||||
{
|
||||
cvm::fatal_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");
|
||||
return 0.;
|
||||
}
|
||||
|
||||
|
||||
std::ostream & colvarbias::write_traj_label (std::ostream &os)
|
||||
{
|
||||
os << " ";
|
||||
if (b_output_energy)
|
||||
os << " E_"
|
||||
<< cvm::wrap_string (this->name, cvm::en_width-2);
|
||||
return os;
|
||||
}
|
||||
|
||||
|
||||
std::ostream & colvarbias::write_traj (std::ostream &os)
|
||||
{
|
||||
os << " ";
|
||||
if (b_output_energy)
|
||||
os << " "
|
||||
<< bias_energy;
|
||||
return os;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
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||||
char const *key)
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|
|
@ -171,21 +206,18 @@ colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
|
|||
}
|
||||
}
|
||||
|
||||
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 harmonic restraint bias.\n");
|
||||
}
|
||||
|
||||
|
||||
void colvarbias::change_configuration(std::string const &conf)
|
||||
colvarbias_harmonic::~colvarbias_harmonic ()
|
||||
{
|
||||
cvm::fatal_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");
|
||||
return 0.;
|
||||
if (cvm::n_harm_biases > 0)
|
||||
cvm::n_harm_biases -= 1;
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -379,6 +411,15 @@ cvm::real colvarbias_harmonic::update()
|
|||
colvar_centers[i]))+"\n");
|
||||
}
|
||||
|
||||
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 harmonic bias \""+
|
||||
this->name+"\": "+cvm::to_str (colvar_forces)+".\n");
|
||||
|
|
@ -442,6 +483,11 @@ std::istream & colvarbias_harmonic::read_restart (std::istream &is)
|
|||
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 harmonic bias \""+
|
||||
|
|
@ -484,9 +530,61 @@ std::ostream & colvarbias_harmonic::write_restart (std::ostream &os)
|
|||
<< stage << "\n";
|
||||
}
|
||||
|
||||
if (b_output_acc_work) {
|
||||
os << " accumulatedWork " << acc_work << "\n";
|
||||
}
|
||||
|
||||
os << " }\n"
|
||||
<< "}\n\n";
|
||||
|
||||
return os;
|
||||
}
|
||||
|
||||
|
||||
std::ostream & colvarbias_harmonic::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_harmonic::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;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -52,6 +52,13 @@ public:
|
|||
/// Write the bias configuration to a restart file
|
||||
virtual std::ostream & write_restart (std::ostream &os) = 0;
|
||||
|
||||
/// 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);
|
||||
|
||||
|
||||
protected:
|
||||
|
||||
/// \brief Pointers to collective variables to which the bias is
|
||||
|
|
@ -62,10 +69,12 @@ protected:
|
|||
/// \brief Current forces from this bias to the colvars
|
||||
std::vector<colvarvalue> colvar_forces;
|
||||
|
||||
/// \brief Current energy of this bias (colvar_forces should be
|
||||
/// obtained by deriving this)
|
||||
/// \brief Current energy of this bias (colvar_forces should be obtained by deriving this)
|
||||
cvm::real bias_energy;
|
||||
|
||||
/// Whether to write the current bias energy from this bias to the trajectory file
|
||||
bool b_output_energy;
|
||||
|
||||
/// \brief Whether this bias has already accumulated information
|
||||
/// (when relevant)
|
||||
bool has_data;
|
||||
|
|
@ -94,11 +103,17 @@ public:
|
|||
/// 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_harmonic (std::string const &conf, char const *key);
|
||||
|
||||
/// Destructor
|
||||
virtual inline ~colvarbias_harmonic() {}
|
||||
virtual ~colvarbias_harmonic();
|
||||
|
||||
|
||||
protected:
|
||||
|
|
@ -109,27 +124,9 @@ protected:
|
|||
/// \brief Restraint centers without wrapping or constraints applied
|
||||
std::vector<colvarvalue> colvar_centers_raw;
|
||||
|
||||
/// \brief Restraint force constant
|
||||
cvm::real force_k;
|
||||
|
||||
/// \brief Moving target?
|
||||
bool b_chg_centers;
|
||||
|
||||
/// \brief Changing force constant?
|
||||
bool b_chg_force_k;
|
||||
|
||||
/// \brief Restraint force constant (target value)
|
||||
cvm::real target_force_k;
|
||||
|
||||
/// \brief Equilibration steps for restraint FE calculation through TI
|
||||
cvm::real target_equil_steps;
|
||||
|
||||
/// \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 New restraint centers
|
||||
std::vector<colvarvalue> target_centers;
|
||||
|
||||
|
|
@ -137,12 +134,41 @@ protected:
|
|||
/// (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 Number of steps required to reach the target force constant
|
||||
/// or restraint centers
|
||||
size_t target_nsteps;
|
||||
/// \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
|
||||
|
|
@ -151,9 +177,9 @@ protected:
|
|||
/// \brief Number of current stage of the perturbation
|
||||
int stage;
|
||||
|
||||
/// \brief Intermediate quantity to compute the restraint free energy
|
||||
/// (in TI, would be the accumulating FE derivative)
|
||||
cvm::real restraint_FE;
|
||||
/// \brief Number of steps required to reach the target force constant
|
||||
/// or restraint centers
|
||||
size_t target_nsteps;
|
||||
};
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -82,6 +82,20 @@ colvarbias_abf::colvarbias_abf (std::string const &conf, char const *key)
|
|||
// and make it just a warning if some parameter is set?
|
||||
}
|
||||
|
||||
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.");
|
||||
}
|
||||
for (size_t i=0; i<colvars.size(); i++) {
|
||||
if (max_force[i] < 0.0) {
|
||||
cvm::fatal_error ("Error: maxForce should be non-negative.");
|
||||
}
|
||||
}
|
||||
cap_force = true;
|
||||
} else {
|
||||
cap_force = false;
|
||||
}
|
||||
|
||||
bin.assign (colvars.size(), 0);
|
||||
force_bin.assign (colvars.size(), 0);
|
||||
force = new cvm::real [colvars.size()];
|
||||
|
|
@ -114,6 +128,9 @@ colvarbias_abf::~colvarbias_abf()
|
|||
}
|
||||
|
||||
delete [] force;
|
||||
|
||||
if (cvm::n_abf_biases > 0)
|
||||
cvm::n_abf_biases -= 1;
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -180,15 +197,21 @@ cvm::real colvarbias_abf::update()
|
|||
const cvm::real * grad = &(gradients->value (bin));
|
||||
|
||||
if ( fact != 0.0 ) {
|
||||
|
||||
if ( (colvars.size() == 1) && colvars[0]->periodic_boundaries() ) {
|
||||
// Enforce a zero-mean bias on periodic, 1D coordinates
|
||||
colvar_forces[0].real_value += fact * (grad[0] / cvm::real (count) - gradients->average ());
|
||||
// in other words: boundary condition is that the biasing potential is periodic
|
||||
colvar_forces[0].real_value = fact * (grad[0] / cvm::real (count) - gradients->average ());
|
||||
} else {
|
||||
for (size_t i=0; i<colvars.size(); i++) {
|
||||
// subtracting the mean force (opposite of the FE gradient) means adding the gradient
|
||||
colvar_forces[i].real_value += fact * grad[i] / cvm::real (count);
|
||||
// without .real_value, the above would do (cheap) runtime type checking
|
||||
colvar_forces[i].real_value = fact * grad[i] / cvm::real (count);
|
||||
}
|
||||
}
|
||||
if (cap_force) {
|
||||
for (size_t i=0; i<colvars.size(); i++) {
|
||||
if ( colvar_forces[i].real_value * colvar_forces[i].real_value > max_force[i] * max_force[i] ) {
|
||||
colvar_forces[i].real_value = (colvar_forces[i].real_value > 0 ? max_force[i] : -1.0 * max_force[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -203,7 +226,7 @@ cvm::real colvarbias_abf::update()
|
|||
// otherwise, backup and replace
|
||||
write_gradients_samples (output_prefix + ".hist", (cvm::step_absolute() > 0));
|
||||
}
|
||||
return 0.0; // TODO compute bias energy whenever possible (i.e. 1D with updateBias off)
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -395,6 +418,9 @@ colvarbias_histogram::~colvarbias_histogram()
|
|||
delete grid;
|
||||
grid = NULL;
|
||||
}
|
||||
|
||||
if (cvm::n_histo_biases > 0)
|
||||
cvm::n_histo_biases -= 1;
|
||||
}
|
||||
|
||||
/// Update the grid
|
||||
|
|
|
|||
|
|
@ -46,6 +46,10 @@ private:
|
|||
bool b_history_files;
|
||||
size_t history_freq;
|
||||
|
||||
/// Cap applied biasing force?
|
||||
bool cap_force;
|
||||
std::vector<cvm::real> max_force;
|
||||
|
||||
// Internal data and methods
|
||||
|
||||
std::vector<int> bin, force_bin;
|
||||
|
|
|
|||
|
|
@ -76,7 +76,8 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
|
|||
}
|
||||
|
||||
get_keyval (conf, "keepHills", keep_hills, false);
|
||||
get_keyval (conf, "dumpFreeEnergyFile", dump_fes, true);
|
||||
if (! get_keyval (conf, "writeFreeEnergyFile", dump_fes, true))
|
||||
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++) {
|
||||
|
|
@ -258,6 +259,9 @@ colvarbias_meta::~colvarbias_meta()
|
|||
|
||||
if (hills_traj_os.good())
|
||||
hills_traj_os.close();
|
||||
|
||||
if (cvm::n_meta_biases > 0)
|
||||
cvm::n_meta_biases -= 1;
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,16 @@
|
|||
#ifndef COLVARCOMP_H
|
||||
#define COLVARCOMP_H
|
||||
|
||||
// Declaration of colvar::cvc base class and derived ones.
|
||||
//
|
||||
// Future cvc's could be declared on additional header files.
|
||||
// After the declaration of a new derived class, its metric
|
||||
// functions must be reimplemented as well.
|
||||
// If the new cvc has no symmetry or periodicity,
|
||||
// this can be done straightforwardly by using the macro:
|
||||
// simple_scalar_dist_functions (derived_class)
|
||||
|
||||
|
||||
#include <fstream>
|
||||
#include <cmath>
|
||||
|
||||
|
|
@ -591,7 +601,7 @@ protected:
|
|||
std::vector<cvm::atom_pos> ref_pos;
|
||||
|
||||
/// Geometric center of the reference coordinates
|
||||
cvm::rvector ref_pos_center;
|
||||
cvm::atom_pos ref_pos_center;
|
||||
|
||||
/// Eigenvector (of a normal or essential mode): will always have zero center
|
||||
std::vector<cvm::rvector> eigenvec;
|
||||
|
|
@ -1140,6 +1150,62 @@ public:
|
|||
};
|
||||
|
||||
|
||||
|
||||
// metrics functions for cvc implementations
|
||||
|
||||
// simple definitions of the distance functions; these are useful only
|
||||
// for optimization (the type check performed in the default
|
||||
// colvarcomp functions is skipped)
|
||||
|
||||
// definitions assuming the scalar type
|
||||
|
||||
#define simple_scalar_dist_functions(TYPE) \
|
||||
\
|
||||
inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \
|
||||
colvarvalue const &x2) const \
|
||||
{ \
|
||||
return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
|
||||
} \
|
||||
\
|
||||
inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \
|
||||
colvarvalue const &x2) const \
|
||||
{ \
|
||||
return 2.0 * (x1.real_value - x2.real_value); \
|
||||
} \
|
||||
\
|
||||
inline colvarvalue colvar::TYPE::dist2_rgrad (colvarvalue const &x1, \
|
||||
colvarvalue const &x2) const \
|
||||
{ \
|
||||
return this->dist2_lgrad (x2, x1); \
|
||||
} \
|
||||
\
|
||||
inline cvm::real colvar::TYPE::compare (colvarvalue const &x1, \
|
||||
colvarvalue const &x2) const \
|
||||
{ \
|
||||
return this->dist2_lgrad (x1, x2); \
|
||||
} \
|
||||
\
|
||||
|
||||
simple_scalar_dist_functions (distance)
|
||||
// NOTE: distance_z has explicit functions, see below
|
||||
simple_scalar_dist_functions (distance_xy)
|
||||
simple_scalar_dist_functions (distance_inv)
|
||||
simple_scalar_dist_functions (angle)
|
||||
simple_scalar_dist_functions (coordnum)
|
||||
simple_scalar_dist_functions (selfcoordnum)
|
||||
simple_scalar_dist_functions (h_bond)
|
||||
simple_scalar_dist_functions (gyration)
|
||||
simple_scalar_dist_functions (inertia)
|
||||
simple_scalar_dist_functions (inertia_z)
|
||||
simple_scalar_dist_functions (rmsd)
|
||||
simple_scalar_dist_functions (orientation_angle)
|
||||
simple_scalar_dist_functions (tilt)
|
||||
simple_scalar_dist_functions (eigenvector)
|
||||
// simple_scalar_dist_functions (alpha_dihedrals)
|
||||
simple_scalar_dist_functions (alpha_angles)
|
||||
simple_scalar_dist_functions (dihedPC)
|
||||
|
||||
|
||||
// metrics functions for cvc implementations with a periodicity
|
||||
|
||||
inline cvm::real colvar::dihedral::dist2 (colvarvalue const &x1,
|
||||
|
|
@ -1232,58 +1298,6 @@ inline void colvar::spin_angle::wrap (colvarvalue &x) const
|
|||
return;
|
||||
}
|
||||
|
||||
// simple definitions of the distance functions; these are useful only
|
||||
// for optimization (the type check performed in the default
|
||||
// colvarcomp functions is skipped)
|
||||
|
||||
// definitions assuming the scalar type
|
||||
|
||||
#define simple_scalar_dist_functions(TYPE) \
|
||||
\
|
||||
inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \
|
||||
colvarvalue const &x2) const \
|
||||
{ \
|
||||
return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
|
||||
} \
|
||||
\
|
||||
inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \
|
||||
colvarvalue const &x2) const \
|
||||
{ \
|
||||
return 2.0 * (x1.real_value - x2.real_value); \
|
||||
} \
|
||||
\
|
||||
inline colvarvalue colvar::TYPE::dist2_rgrad (colvarvalue const &x1, \
|
||||
colvarvalue const &x2) const \
|
||||
{ \
|
||||
return this->dist2_lgrad (x2, x1); \
|
||||
} \
|
||||
\
|
||||
inline cvm::real colvar::TYPE::compare (colvarvalue const &x1, \
|
||||
colvarvalue const &x2) const \
|
||||
{ \
|
||||
return this->dist2_lgrad (x1, x2); \
|
||||
} \
|
||||
\
|
||||
|
||||
simple_scalar_dist_functions (distance)
|
||||
// NOTE: distance_z has explicit functions, see below
|
||||
simple_scalar_dist_functions (distance_xy)
|
||||
simple_scalar_dist_functions (distance_inv)
|
||||
simple_scalar_dist_functions (angle)
|
||||
simple_scalar_dist_functions (coordnum)
|
||||
simple_scalar_dist_functions (selfcoordnum)
|
||||
simple_scalar_dist_functions (h_bond)
|
||||
simple_scalar_dist_functions (gyration)
|
||||
simple_scalar_dist_functions (inertia)
|
||||
simple_scalar_dist_functions (inertia_z)
|
||||
simple_scalar_dist_functions (rmsd)
|
||||
simple_scalar_dist_functions (orientation_angle)
|
||||
simple_scalar_dist_functions (tilt)
|
||||
simple_scalar_dist_functions (eigenvector)
|
||||
// simple_scalar_dist_functions (alpha_dihedrals)
|
||||
simple_scalar_dist_functions (alpha_angles)
|
||||
simple_scalar_dist_functions (dihedPC)
|
||||
|
||||
|
||||
// Projected distance
|
||||
// Differences should always be wrapped around 0 (ignoring wrap_center)
|
||||
|
|
@ -1422,9 +1436,6 @@ inline cvm::real colvar::orientation::compare (colvarvalue const &x1,
|
|||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -77,6 +77,9 @@ colvar::coordnum::coordnum (std::string const &conf)
|
|||
x.type (colvarvalue::type_scalar);
|
||||
|
||||
// group1 and group2 are already initialized by distance()
|
||||
if (group1.b_dummy)
|
||||
cvm::fatal_error ("Error: only group2 is allowed to be a dummy atom\n");
|
||||
|
||||
|
||||
// need to specify this explicitly because the distance() constructor
|
||||
// has set it to true
|
||||
|
|
@ -105,7 +108,7 @@ colvar::coordnum::coordnum (std::string const &conf)
|
|||
cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n");
|
||||
}
|
||||
|
||||
get_keyval (conf, "group2CenterOnly", b_group2_center_only, false);
|
||||
get_keyval (conf, "group2CenterOnly", b_group2_center_only, group2.b_dummy);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -121,18 +124,10 @@ void colvar::coordnum::calc_value()
|
|||
{
|
||||
x.real_value = 0.0;
|
||||
|
||||
// these are necessary: for each atom, gradients are summed together
|
||||
// by multiple calls to switching_function()
|
||||
group1.reset_atoms_data();
|
||||
group2.reset_atoms_data();
|
||||
|
||||
group1.read_positions();
|
||||
group2.read_positions();
|
||||
|
||||
if (b_group2_center_only) {
|
||||
|
||||
// create a fake atom to hold the group2 com coordinates
|
||||
cvm::atom group2_com_atom (group2[0]);
|
||||
cvm::atom group2_com_atom;
|
||||
group2_com_atom.pos = group2.center_of_mass();
|
||||
|
||||
if (b_anisotropic) {
|
||||
|
|
@ -165,9 +160,10 @@ void colvar::coordnum::calc_gradients()
|
|||
if (b_group2_center_only) {
|
||||
|
||||
// create a fake atom to hold the group2 com coordinates
|
||||
cvm::atom group2_com_atom (group2[0]);
|
||||
cvm::atom group2_com_atom;
|
||||
group2_com_atom.pos = group2.center_of_mass();
|
||||
|
||||
|
||||
if (b_anisotropic) {
|
||||
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
|
||||
switching_function<true> (r0_vec, en, ed, *ai1, group2_com_atom);
|
||||
|
|
@ -288,14 +284,6 @@ colvar::h_bond::~h_bond()
|
|||
|
||||
void colvar::h_bond::calc_value()
|
||||
{
|
||||
// this is necessary, because switching_function() will sum the new
|
||||
// gradient to the current one
|
||||
acceptor.reset_data();
|
||||
donor.reset_data();
|
||||
|
||||
acceptor.read_position();
|
||||
donor.read_position();
|
||||
|
||||
x.real_value = colvar::coordnum::switching_function<false> (r0, en, ed, acceptor, donor);
|
||||
}
|
||||
|
||||
|
|
@ -315,35 +303,6 @@ void colvar::h_bond::apply_force (colvarvalue const &force)
|
|||
}
|
||||
|
||||
|
||||
// Self-coordination number for a group
|
||||
|
||||
template<bool calculate_gradients>
|
||||
cvm::real colvar::selfcoordnum::switching_function (cvm::real const &r0,
|
||||
int const &en,
|
||||
int const &ed,
|
||||
cvm::atom &A1,
|
||||
cvm::atom &A2)
|
||||
{
|
||||
cvm::rvector const diff = cvm::position_distance (A1.pos, A2.pos);
|
||||
cvm::real const l2 = diff.norm2()/(r0*r0);
|
||||
|
||||
// Assume en and ed are even integers, and avoid sqrt in the following
|
||||
int const en2 = en/2;
|
||||
int const ed2 = ed/2;
|
||||
|
||||
cvm::real const xn = std::pow (l2, en2);
|
||||
cvm::real const xd = std::pow (l2, ed2);
|
||||
cvm::real const func = (1.0-xn)/(1.0-xd);
|
||||
|
||||
if (calculate_gradients) {
|
||||
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
|
||||
cvm::rvector const dl2dx = (2.0/(r0*r0))*diff;
|
||||
A1.grad += (-1.0)*dFdl2*dl2dx;
|
||||
A2.grad += dFdl2*dl2dx;
|
||||
}
|
||||
|
||||
return func;
|
||||
}
|
||||
|
||||
|
||||
colvar::selfcoordnum::selfcoordnum (std::string const &conf)
|
||||
|
|
@ -379,13 +338,9 @@ void colvar::selfcoordnum::calc_value()
|
|||
{
|
||||
x.real_value = 0.0;
|
||||
|
||||
// for each atom, gradients are summed by multiple calls to switching_function()
|
||||
group1.reset_atoms_data();
|
||||
group1.read_positions();
|
||||
|
||||
for (size_t i = 0; i < group1.size() - 1; i++)
|
||||
for (size_t j = i + 1; j < group1.size(); j++)
|
||||
x.real_value += switching_function<false> (r0, en, ed, group1[i], group1[j]);
|
||||
x.real_value += colvar::coordnum::switching_function<false> (r0, en, ed, group1[i], group1[j]);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -393,7 +348,7 @@ void colvar::selfcoordnum::calc_gradients()
|
|||
{
|
||||
for (size_t i = 0; i < group1.size() - 1; i++)
|
||||
for (size_t j = i + 1; j < group1.size(); j++)
|
||||
switching_function<true> (r0, en, ed, group1[i], group1[j]);
|
||||
colvar::coordnum::switching_function<true> (r0, en, ed, group1[i], group1[j]);
|
||||
}
|
||||
|
||||
void colvar::selfcoordnum::apply_force (colvarvalue const &force)
|
||||
|
|
|
|||
|
|
@ -522,7 +522,7 @@ colvar::gyration::gyration (std::string const &conf)
|
|||
cvm::log ("WARNING: explicit fitting parameters were provided for atom group \"atoms\".");
|
||||
} else {
|
||||
atoms.b_center = true;
|
||||
atoms.ref_pos.assign (1, cvm::rvector (0.0, 0.0, 0.0));
|
||||
atoms.ref_pos.assign (1, cvm::atom_pos (0.0, 0.0, 0.0));
|
||||
}
|
||||
|
||||
x.type (colvarvalue::type_scalar);
|
||||
|
|
@ -991,7 +991,7 @@ colvar::eigenvector::eigenvector (std::string const &conf)
|
|||
"and eigenvector must be defined.\n");
|
||||
}
|
||||
|
||||
cvm::rvector eig_center (0.0, 0.0, 0.0);
|
||||
cvm::atom_pos eig_center (0.0, 0.0, 0.0);
|
||||
for (size_t i = 0; i < atoms.size(); i++) {
|
||||
eig_center += eigenvec[i];
|
||||
}
|
||||
|
|
|
|||
|
|
@ -15,8 +15,8 @@ colvarmodule::colvarmodule (char const *config_filename,
|
|||
proxy = proxy_in;
|
||||
parse = new colvarparse();
|
||||
} else {
|
||||
cvm::fatal_error ("Error: trying to allocate twice the collective "
|
||||
"variable module.\n");
|
||||
cvm::fatal_error ("Error: trying to allocate the collective "
|
||||
"variable module twice.\n");
|
||||
}
|
||||
|
||||
cvm::log (cvm::line_marker);
|
||||
|
|
@ -44,6 +44,11 @@ colvarmodule::colvarmodule (char const *config_filename,
|
|||
config_s.close();
|
||||
}
|
||||
|
||||
std::string index_file_name;
|
||||
if (parse->get_keyval (conf, "indexFile", index_file_name)) {
|
||||
read_index_file (index_file_name.c_str());
|
||||
}
|
||||
|
||||
parse->get_keyval (conf, "analysis", b_analysis, false);
|
||||
|
||||
parse->get_keyval (conf, "debugGradientsStepSize", debug_gradients_step_size, 1.0e-07,
|
||||
|
|
@ -84,8 +89,6 @@ colvarmodule::colvarmodule (char const *config_filename,
|
|||
(output_prefix.size() ?
|
||||
std::string (output_prefix+".colvars.traj") :
|
||||
std::string ("colvars.traj"));
|
||||
cvm::log ("The trajectory file will be \""+
|
||||
cv_traj_name+"\".\n");
|
||||
|
||||
if (cv_traj_freq) {
|
||||
// open trajectory file
|
||||
|
|
@ -94,6 +97,8 @@ colvarmodule::colvarmodule (char const *config_filename,
|
|||
"\".\n");
|
||||
cv_traj_os.open (cv_traj_name.c_str(), std::ios::app);
|
||||
} else {
|
||||
cvm::log ("Writing to colvar trajectory file \""+cv_traj_name+
|
||||
"\".\n");
|
||||
proxy->backup_file (cv_traj_name.c_str());
|
||||
cv_traj_os.open (cv_traj_name.c_str(), std::ios::out);
|
||||
}
|
||||
|
|
@ -478,6 +483,11 @@ void colvarmodule::calc() {
|
|||
cvi++) {
|
||||
(*cvi)->write_traj_label (cv_traj_os);
|
||||
}
|
||||
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
||||
bi != biases.end();
|
||||
bi++) {
|
||||
(*bi)->write_traj_label (cv_traj_os);
|
||||
}
|
||||
cv_traj_os << "\n";
|
||||
if (cvm::debug())
|
||||
cv_traj_os.flush();
|
||||
|
|
@ -494,6 +504,11 @@ void colvarmodule::calc() {
|
|||
cvi++) {
|
||||
(*cvi)->write_traj (cv_traj_os);
|
||||
}
|
||||
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
||||
bi != biases.end();
|
||||
bi++) {
|
||||
(*bi)->write_traj (cv_traj_os);
|
||||
}
|
||||
cv_traj_os << "\n";
|
||||
if (cvm::debug())
|
||||
cv_traj_os.flush();
|
||||
|
|
@ -542,6 +557,14 @@ void colvarmodule::analyze()
|
|||
|
||||
}
|
||||
|
||||
void colvarmodule::setup()
|
||||
{
|
||||
// loop over all components of all colvars to reset masses of all groups
|
||||
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
||||
cvi != colvars.end(); cvi++) {
|
||||
(*cvi)->setup();
|
||||
}
|
||||
}
|
||||
|
||||
colvarmodule::~colvarmodule()
|
||||
{
|
||||
|
|
@ -721,6 +744,55 @@ void cvm::exit (std::string const &message)
|
|||
}
|
||||
|
||||
|
||||
void cvm::read_index_file (char const *filename)
|
||||
{
|
||||
std::ifstream is (filename);
|
||||
if (!is.good())
|
||||
fatal_error ("Error: in opening index file \""+
|
||||
std::string (filename)+"\".\n");
|
||||
// std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
|
||||
// std::list<std::vector<int> >::iterator lists_i = cvm::index_groups.begin();
|
||||
while (is.good()) {
|
||||
char open, close;
|
||||
std::string group_name;
|
||||
if ( (is >> open) && (open == '[') &&
|
||||
(is >> group_name) &&
|
||||
(is >> close) && (close == ']') ) {
|
||||
cvm::index_group_names.push_back (group_name);
|
||||
cvm::index_groups.push_back (std::vector<int> ());
|
||||
} else {
|
||||
cvm::fatal_error ("Error: in parsing index file \""+
|
||||
std::string (filename)+"\".\n");
|
||||
}
|
||||
|
||||
int atom_number = 1;
|
||||
size_t pos = is.tellg();
|
||||
while ( (is >> atom_number) && (atom_number > 0) ) {
|
||||
(cvm::index_groups.back()).push_back (atom_number);
|
||||
pos = is.tellg();
|
||||
}
|
||||
is.clear();
|
||||
is.seekg (pos, std::ios::beg);
|
||||
std::string delim;
|
||||
if ( (is >> delim) && (delim == "[") ) {
|
||||
// new group
|
||||
is.clear();
|
||||
is.seekg (pos, std::ios::beg);
|
||||
} else {
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
cvm::log ("The following index groups were read from the index file \""+
|
||||
std::string (filename)+"\":\n");
|
||||
std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
|
||||
std::list<std::vector<int> >::iterator lists_i = cvm::index_groups.begin();
|
||||
for ( ; names_i != cvm::index_group_names.end() ; names_i++, lists_i++) {
|
||||
cvm::log (" "+(*names_i)+" ("+cvm::to_str (lists_i->size())+" atoms).\n");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
// static pointers
|
||||
std::vector<colvar *> colvarmodule::colvars;
|
||||
|
|
@ -741,6 +813,8 @@ size_t colvarmodule::cv_traj_freq = 0;
|
|||
size_t colvarmodule::depth = 0;
|
||||
bool colvarmodule::b_analysis = false;
|
||||
cvm::real colvarmodule::rotation::crossing_threshold = 1.0E-04;
|
||||
std::list<std::string> colvarmodule::index_group_names;
|
||||
std::list<std::vector<int> > colvarmodule::index_groups;
|
||||
|
||||
|
||||
// file name prefixes
|
||||
|
|
@ -932,15 +1006,13 @@ cvm::quaternion::position_derivative_inner (cvm::rvector const &pos,
|
|||
|
||||
|
||||
|
||||
|
||||
|
||||
// Calculate the optimal rotation between two groups, and implement it
|
||||
// as a quaternion. The method is the one documented in: Coutsias EA,
|
||||
// Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput
|
||||
// Chem. 25(15):1849-57 (2004) DOI: 10.1002/jcc.20110 PubMed: 15376254
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
void colvarmodule::rotation::build_matrix (std::vector<cvm::atom_pos> const &pos1,
|
||||
std::vector<cvm::atom_pos> const &pos2,
|
||||
matrix2d<cvm::real, 4, 4> &S)
|
||||
|
|
@ -1068,7 +1140,8 @@ void colvarmodule::rotation::calc_optimal_rotation
|
|||
if (q_old.norm2() > 0.0) {
|
||||
q.match (q_old);
|
||||
if (q_old.inner (q) < (1.0 - crossing_threshold)) {
|
||||
cvm::log ("Warning: discontinuous rotation!\n");
|
||||
cvm::log ("Warning: one molecular orientation has changed by more than "+
|
||||
cvm::to_str (crossing_threshold)+": discontinuous rotation ?\n");
|
||||
}
|
||||
}
|
||||
q_old = q;
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
#define COLVARMODULE_H
|
||||
|
||||
#ifndef COLVARS_VERSION
|
||||
#define COLVARS_VERSION "2013-04-17"
|
||||
#define COLVARS_VERSION "2013-06-19"
|
||||
#endif
|
||||
|
||||
#ifndef COLVARS_DEBUG
|
||||
|
|
@ -159,6 +159,7 @@ public:
|
|||
/// \param restart_name (optional) Restart file name
|
||||
colvarmodule (char const *config_name,
|
||||
colvarproxy *proxy_in);
|
||||
|
||||
/// Destructor
|
||||
~colvarmodule();
|
||||
|
||||
|
|
@ -168,6 +169,11 @@ public:
|
|||
/// Initialize collective variable biases
|
||||
void init_biases (std::string const &conf);
|
||||
|
||||
/// 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();
|
||||
|
||||
/// 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);
|
||||
|
|
@ -290,6 +296,16 @@ public:
|
|||
atom_pos const &ref_pos);
|
||||
|
||||
|
||||
/// \brief Names of groups from a Gromacs .ndx file to be read at startup
|
||||
static std::list<std::string> index_group_names;
|
||||
|
||||
/// \brief Groups from a Gromacs .ndx file read at startup
|
||||
static std::list<std::vector<int> > index_groups;
|
||||
|
||||
/// \brief Read a Gromacs .ndx file
|
||||
static void 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
|
||||
|
|
|
|||
|
|
@ -371,8 +371,8 @@ void colvarparse::check_keywords (std::string &conf, char const *key)
|
|||
std::string uk;
|
||||
std::istringstream line_is (line);
|
||||
line_is >> uk;
|
||||
if (cvm::debug())
|
||||
cvm::log ("Checking the validity of \""+uk+"\" from line:\n" + line);
|
||||
// if (cvm::debug())
|
||||
// cvm::log ("Checking the validity of \""+uk+"\" from line:\n" + line);
|
||||
uk = to_lower_cppstr (uk);
|
||||
|
||||
bool found_keyword = false;
|
||||
|
|
|
|||
|
|
@ -16,6 +16,12 @@ public:
|
|||
/// Pointer to the instance of colvarmodule
|
||||
colvarmodule *colvars;
|
||||
|
||||
/// Default destructor
|
||||
virtual inline ~colvarproxy() {}
|
||||
|
||||
|
||||
// **************** SYSTEM-WIDE PHYSICAL QUANTITIES ****************
|
||||
|
||||
/// \brief Value of the unit for atomic coordinates with respect to
|
||||
/// angstroms (used by some variables for hard-coded default values)
|
||||
virtual cvm::real unit_angstrom() = 0;
|
||||
|
|
@ -29,21 +35,11 @@ public:
|
|||
/// \brief Time step of the simulation (fs)
|
||||
virtual cvm::real dt() = 0;
|
||||
|
||||
/// Pass restraint energy value for current timestep to MD engine
|
||||
virtual void add_energy (cvm::real energy) = 0;
|
||||
/// \brief Pseudo-random number with Gaussian distribution
|
||||
virtual cvm::real rand_gaussian (void) = 0;
|
||||
|
||||
/// Tell the proxy whether system forces are needed
|
||||
virtual void request_system_force (bool yesno) = 0;
|
||||
|
||||
/// Print a message to the main log
|
||||
virtual void log (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;
|
||||
|
||||
/// Print a message to the main log and exit normally
|
||||
virtual void exit (std::string const &message) = 0;
|
||||
|
||||
// **************** SIMULATION PARAMETERS ****************
|
||||
|
||||
/// \brief Prefix to be used for input files (restarts, not
|
||||
/// configuration)
|
||||
|
|
@ -59,21 +55,28 @@ public:
|
|||
/// \brief Restarts will be fritten each time this number of steps has passed
|
||||
virtual size_t restart_frequency() = 0;
|
||||
|
||||
|
||||
|
||||
// **************** ACCESS ATOMIC DATA ****************
|
||||
|
||||
/// Pass restraint energy value for current timestep to MD engine
|
||||
virtual void add_energy (cvm::real energy) = 0;
|
||||
|
||||
/// Tell the proxy whether system forces are needed (may not always be available)
|
||||
virtual void request_system_force (bool yesno) = 0;
|
||||
|
||||
|
||||
|
||||
// **************** PERIODIC BOUNDARY CONDITIONS ****************
|
||||
|
||||
/// \brief Get the simple distance vector between two positions
|
||||
/// (with periodic boundary conditions handled transparently)
|
||||
/// \brief Get the PBC-aware distance vector between two positions
|
||||
virtual cvm::rvector position_distance (cvm::atom_pos const &pos1,
|
||||
cvm::atom_pos const &pos2) = 0;
|
||||
|
||||
/// \brief Get the square distance between two positions (with
|
||||
/// periodic boundary conditions handled transparently)
|
||||
///
|
||||
/// Note: in the case of periodic boundary conditions, this provides
|
||||
/// an analytical square distance (while taking the square of
|
||||
/// position_distance() would produce leads to a cusp)
|
||||
/// \brief Get the PBC-aware square distance between two positions;
|
||||
/// may be implemented independently from position_distance() for optimization purposes
|
||||
virtual cvm::real position_dist2 (cvm::atom_pos const &pos1,
|
||||
cvm::atom_pos const &pos2) = 0;
|
||||
cvm::atom_pos const &pos2);
|
||||
|
||||
/// \brief Get the closest periodic image to a reference position
|
||||
/// \param pos The position to look for the closest periodic image
|
||||
|
|
@ -89,6 +92,18 @@ public:
|
|||
cvm::atom_pos const &ref_pos);
|
||||
|
||||
|
||||
|
||||
// **************** 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 exit with error code
|
||||
virtual void fatal_error (std::string const &message) = 0;
|
||||
|
||||
/// Print a message to the main log and exit normally
|
||||
virtual void exit (std::string const &message) = 0;
|
||||
|
||||
/// \brief Read atom identifiers from a file \param filename name of
|
||||
/// the file (usually a PDB) \param atoms array to which atoms read
|
||||
/// from "filename" will be appended \param pdb_field (optiona) if
|
||||
|
|
@ -97,7 +112,7 @@ public:
|
|||
virtual void load_atoms (char const *filename,
|
||||
std::vector<cvm::atom> &atoms,
|
||||
std::string const pdb_field,
|
||||
double const pdb_field_value = 0.0) = 0;
|
||||
double const pdb_field_value = 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
|
||||
|
|
@ -108,14 +123,9 @@ public:
|
|||
std::string const pdb_field,
|
||||
double const pdb_field_value = 0.0) = 0;
|
||||
|
||||
/// \brief Rename the given file, under the convention provided by
|
||||
/// the MD program
|
||||
virtual void backup_file (char const *filename) = 0;
|
||||
/// \brief Rename the given file, before overwriting it
|
||||
virtual void backup_file (char const *filename) {}
|
||||
|
||||
/// \brief Pseudo-random number with Gaussian distribution
|
||||
virtual cvm::real rand_gaussian (void) = 0;
|
||||
|
||||
virtual inline ~colvarproxy() {}
|
||||
};
|
||||
|
||||
|
||||
|
|
@ -128,6 +138,12 @@ inline void colvarproxy::select_closest_images (std::vector<cvm::atom_pos> &pos,
|
|||
}
|
||||
}
|
||||
|
||||
inline cvm::real colvarproxy::position_dist2 (cvm::atom_pos const &pos1,
|
||||
cvm::atom_pos const &pos2)
|
||||
{
|
||||
return (position_distance (pos1, pos2)).norm2();
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -242,7 +242,7 @@ std::istream & operator >> (std::istream &is, colvarvalue &x)
|
|||
}
|
||||
|
||||
|
||||
size_t colvarvalue::output_width (size_t const &real_width)
|
||||
size_t colvarvalue::output_width (size_t const &real_width) const
|
||||
{
|
||||
switch (this->value_type) {
|
||||
case colvarvalue::type_scalar:
|
||||
|
|
|
|||
|
|
@ -265,10 +265,10 @@ public:
|
|||
/// with a different type to this object
|
||||
void error_rside (Type const &vt) const;
|
||||
|
||||
///<EFBFBD>Give the number of characters required to output this
|
||||
/// 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);
|
||||
size_t output_width (size_t const &real_width) const;
|
||||
|
||||
|
||||
// optimized routines for operations with an array; xv and inner as
|
||||
|
|
|
|||
Loading…
Reference in New Issue