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Update Colvars library to version 2023-05-01

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This update consists exclusively of bugfixes or maintenance-related changes.

The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS:

- 532 Add XYZ trajectory reading feature
  https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin)

- 531 Delete objects quietly, unless explicitly requested via script (including VMD)
  https://github.com/Colvars/colvars/pull/531 (@giacomofiorin)

- 530 Append newline to log and error messages if not already present
  https://github.com/Colvars/colvars/pull/530 (@giacomofiorin)

- 528 Forward-declare OpenMP lock
  https://github.com/Colvars/colvars/pull/528 (@giacomofiorin)

- 527 Remove unneeded STL container
  https://github.com/Colvars/colvars/pull/527 (@giacomofiorin)

- 526 Allow collecting configuration files and strings before setting up interface
  https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin)

- 523 Fallback to linearCombination when customFunction is missing in customColvar
  https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin)

- 522 Use iostream::fail() to check for I/O error
  https://github.com/Colvars/colvars/pull/522 (@jhenin)

- 520 Fix ref count
  https://github.com/Colvars/colvars/pull/520 (@giacomofiorin)

- 513 Set target temperature through a common code path
  https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin)

- 509 Safer detection of Windows with recent Microsoft Visual Studio versions
  https://github.com/Colvars/colvars/pull/509 (@akohlmey)

- 508 Update LAMMPS patching method to reflect Lepton availability
  https://github.com/Colvars/colvars/pull/508 (@giacomofiorin)

- 497 Increase the precision of write_multicol
  https://github.com/Colvars/colvars/pull/497 (@HanatoK)

- 496 Only perform MTS automatic enable/disable for timeStepFactor > 1
  https://github.com/Colvars/colvars/pull/496 (@giacomofiorin)

- 493 Remove unused branch of quaternion input function
  https://github.com/Colvars/colvars/pull/493 (@giacomofiorin)

- 489 Ensure there are spaces between the fields in the header
  https://github.com/Colvars/colvars/pull/489 (@HanatoK)

- 487 Use map of output streams, and return references to its elements
  https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin)

- 486 Remember first step of moving restraint
  https://github.com/Colvars/colvars/pull/486 (@jhenin)

- 485 Add decoupling option for moving restraints
  https://github.com/Colvars/colvars/pull/485 (@jhenin)

- 483 Update Lepton via patching procedure
  https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)

- 481 Make file-reading operations of input data abstractable
  https://github.com/Colvars/colvars/pull/481 (@giacomofiorin)

Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
This commit is contained in:
Giacomo Fiorin
2023-05-17 13:29:00 -04:00
parent 166301180b
commit 377c652a83
53 changed files with 2575 additions and 2273 deletions
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lib/colvars/Makefile.common
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@ -50,7 +50,9 @@ COLVARS_SRCS = \
colvarparams.cpp \
colvarparse.cpp \
colvarproxy.cpp \
colvarproxy_io.cpp \
colvarproxy_replicas.cpp \
colvarproxy_system.cpp \
colvarproxy_tcl.cpp \
colvarproxy_volmaps.cpp \
colvarscript.cpp \

504
lib/colvars/Makefile.deps
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@ -1,371 +1,140 @@
$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvarparse.h colvarparams.h \
colvaratoms.h colvardeps.h
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvarparse.h colvarparams.h colvaratoms.h \
colvardeps.h
$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
colvars_version.h colvar.h colvarvalue.h colvartypes.h colvarparse.h \
colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarbias_abf.h colvarproxy.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvarbias.h colvargrid.h \
colvar_UIestimator.h
colvarparams.h colvardeps.h colvarbias_abf.h colvarproxy.h \
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvarbias.h colvargrid.h colvar_UIestimator.h
$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \
colvarparse.h colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarbias_alb.h
colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h
$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvarbias.h colvar.h \
colvarparse.h colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvargrid.h
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvarbias.h colvar.h colvarparse.h colvarparams.h \
colvardeps.h colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h \
colvarparse.h colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarbias_histogram.h colvarbias.h \
colvargrid.h
colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
colvarbias_histogram.h colvarbias.h colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_histogram_reweight_amd.o: \
colvarbias_histogram_reweight_amd.cpp \
colvarbias_histogram_reweight_amd.h colvarbias_histogram.h colvarbias.h \
colvar.h colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
colvarparse.h colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvargrid.h colvarproxy.h \
colvarproxy_tcl.h colvarproxy_volmaps.h
colvarparse.h colvarparams.h colvardeps.h colvargrid.h colvarproxy.h \
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h
$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarparse.h \
colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarbias_meta.h colvarbias.h \
colvargrid.h
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
colvarbias_meta.h colvarbias.h colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h
colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvarbias_restraint.h colvarbias.h colvar.h \
colvarparse.h colvarparams.h colvardeps.h
$(COLVARS_OBJ_DIR)colvarcomp_alchlambda.o: colvarcomp_alchlambda.cpp \
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
colvarparse.h colvarparams.h colvar.h colvardeps.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
colvarparse.h colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
colvarparams.h colvar.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvar.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvar_arithmeticpath.h \
colvar_geometricpath.h
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvardeps.h colvar.h colvarcomp.h \
colvar_arithmeticpath.h colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
colvarparams.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
colvarparse.h colvarparams.h colvar.h colvardeps.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
colvarparams.h colvar.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_neuralnetwork.o: \
colvarcomp_neuralnetwork.cpp colvarmodule.h colvars_version.h \
colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h \
colvar_neuralnetworkcompute.h
$(COLVARS_OBJ_DIR)colvarcomp_combination.o: colvarcomp_combination.cpp \
colvarcomp.h colvarmodule.h colvars_version.h colvar.h colvarvalue.h \
colvartypes.h colvarparse.h colvarparams.h colvardeps.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvaratoms.h colvarproxy.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
colvar_geometricpath.h
colvartypes.h colvarparse.h colvarparams.h colvardeps.h colvaratoms.h \
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
colvarparse.h colvarparams.h colvar.h colvardeps.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
colvarparse.h colvarparams.h colvar.h colvardeps.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvarcomp_volmaps.o: colvarcomp_volmaps.cpp \
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
colvarparse.h colvarparams.h colvar.h colvardeps.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
colvaratoms.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
colvar_geometricpath.h
$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h colvarscript.h \
colvarbias.h colvarscript_commands.h colvarscript_commands_colvar.h \
colvarscript_commands_bias.h
$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.h \
colvarparams.h
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h
$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
colvarparams.h colvar.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar_arithmeticpath.h colvar_geometricpath.h colvargrid.h
colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h \
colvargrid.h colvargrid_def.h
$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
colvarparams.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvar.h colvardeps.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarbias.h colvarbias_abf.h \
colvargrid.h colvar_UIestimator.h colvarbias_alb.h \
colvarbias_histogram.h colvarbias_histogram_reweight_amd.h \
colvarbias_meta.h colvarbias_restraint.h colvarscript.h \
colvarscript_commands.h colvarscript_commands_colvar.h \
colvarscript_commands_bias.h colvaratoms.h colvarcomp.h \
colvar_arithmeticpath.h colvar_geometricpath.h colvarmodule_refs.h
colvarparams.h colvarproxy.h colvarproxy_io.h colvarproxy_system.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvardeps.h \
colvarbias.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \
colvarbias_alb.h colvarbias_histogram.h \
colvarbias_histogram_reweight_amd.h colvarbias_meta.h \
colvarbias_restraint.h colvarscript.h colvarscript_commands.h \
colvarscript_commands_colvar.h colvarscript_commands_bias.h \
colvaratoms.h colvarcomp.h colvar_arithmeticpath.h \
colvar_geometricpath.h colvarmodule_refs.h
$(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
@ -373,97 +142,53 @@ $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
colvarparams.h
$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvarscript.h colvarbias.h \
colvar.h colvarparse.h colvarparams.h colvardeps.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarscript_commands.h \
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvarscript.h colvarbias.h colvar.h colvarparse.h \
colvarparams.h colvardeps.h colvarscript_commands.h \
colvarscript_commands_colvar.h colvarscript_commands_bias.h \
colvaratoms.h colvarmodule_utils.h
$(COLVARS_OBJ_DIR)colvarproxy_io.o: colvarproxy_io.cpp colvarmodule.h \
colvars_version.h colvarproxy_io.h
$(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h
colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h
$(COLVARS_OBJ_DIR)colvarproxy_system.o: colvarproxy_system.cpp \
colvarmodule.h colvars_version.h colvartypes.h colvarproxy_system.h
$(COLVARS_OBJ_DIR)colvarproxy_tcl.o: colvarproxy_tcl.cpp colvarmodule.h \
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvaratoms.h colvarparse.h \
colvarparams.h colvardeps.h
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvaratoms.h colvarparse.h colvarparams.h \
colvardeps.h
$(COLVARS_OBJ_DIR)colvarproxy_volmaps.o: colvarproxy_volmaps.cpp \
colvarmodule.h colvars_version.h colvarproxy_volmaps.h \
colvarmodule_utils.h
$(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarproxy.h \
colvarmodule.h colvars_version.h colvartypes.h colvarvalue.h \
colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.h \
colvarparams.h colvarscript.h colvarbias.h colvar.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarscript_commands.h \
colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \
colvarscript_commands_colvar.h colvarscript_commands_bias.h
$(COLVARS_OBJ_DIR)colvarscript_commands.o: colvarscript_commands.cpp \
colvarproxy.h colvarmodule.h colvars_version.h colvartypes.h \
colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h \
colvarparse.h colvarparams.h colvarscript.h colvarbias.h colvar.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarscript_commands.h \
colvarvalue.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \
colvarscript_commands_colvar.h colvarscript_commands_bias.h
$(COLVARS_OBJ_DIR)colvarscript_commands_bias.o: \
colvarscript_commands_bias.cpp colvarproxy.h colvarmodule.h \
colvars_version.h colvartypes.h colvarvalue.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
colvarscript.h colvarbias.h colvar.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarscript_commands.h \
colvarscript_commands_colvar.h colvarscript_commands_bias.h
colvars_version.h colvartypes.h colvarvalue.h colvarproxy_io.h \
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvardeps.h colvarparse.h colvarparams.h colvarscript.h colvarbias.h \
colvar.h colvarscript_commands.h colvarscript_commands_colvar.h \
colvarscript_commands_bias.h
$(COLVARS_OBJ_DIR)colvarscript_commands_colvar.o: \
colvarscript_commands_colvar.cpp colvarproxy.h colvarmodule.h \
colvars_version.h colvartypes.h colvarvalue.h colvarproxy_tcl.h \
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
colvarscript.h colvarbias.h colvar.h ../lepton/include/Lepton.h \
../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarscript_commands.h \
colvarscript_commands_colvar.h colvarscript_commands_bias.h
colvars_version.h colvartypes.h colvarvalue.h colvarproxy_io.h \
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
colvardeps.h colvarparse.h colvarparams.h colvarscript.h colvarbias.h \
colvar.h colvarscript_commands.h colvarscript_commands_colvar.h \
colvarscript_commands_bias.h
$(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \
colvarparams.h ../../src/math_eigen_impl.h
@ -471,15 +196,6 @@ $(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h
$(COLVARS_OBJ_DIR)colvar_neuralnetworkcompute.o: \
colvar_neuralnetworkcompute.cpp colvar_neuralnetworkcompute.h \
../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/windowsIncludes.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/ExpressionProgram.h \
../lepton/include/lepton/ExpressionTreeNode.h \
../lepton/include/lepton/Operation.h \
../lepton/include/lepton/CustomFunction.h \
../lepton/include/lepton/Exception.h \
../lepton/include/lepton/ParsedExpression.h \
../lepton/include/lepton/Parser.h colvarparse.h colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
colvarparse.h colvarmodule.h colvars_version.h colvarvalue.h \
colvartypes.h colvarparams.h colvarproxy.h colvarproxy_io.h \
colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h

54
lib/colvars/colvar.cpp
View File

@ -10,6 +10,8 @@
#include <list>
#include <vector>
#include <algorithm>
#include <iostream>
#include <iomanip>
#include "colvarmodule.h"
#include "colvarvalue.h"
@ -24,8 +26,6 @@ std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)
colvar::colvar()
{
runave_os = NULL;
prev_timestep = -1L;
after_restart = false;
kinetic_energy = 0.0;
@ -291,7 +291,6 @@ int colvar::init(std::string const &conf)
enable(f_cv_multiple_ts);
}
// TODO use here information from the CVCs' own natural boundaries
error_code |= init_grid_parameters(conf);
// Detect if we have a single component that is an alchemical lambda
@ -634,6 +633,7 @@ harmonicWalls {\n\
int colvar::init_extended_Lagrangian(std::string const &conf)
{
colvarproxy *proxy = cvm::main()->proxy;
get_keyval_feature(this, conf, "extendedLagrangian", f_cv_extended_Lagrangian, false);
if (is_enabled(f_cv_extended_Lagrangian)) {
@ -646,7 +646,8 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
x_ext.type(colvarvalue::type_notset);
v_ext.type(value());
fr.type(value());
const bool temp_provided = get_keyval(conf, "extendedTemp", temp, cvm::temperature());
const bool temp_provided = get_keyval(conf, "extendedTemp", temp,
proxy->target_temperature());
if (is_enabled(f_cv_external)) {
// In the case of an "external" coordinate, there is no coupling potential:
// only the fictitious mass is meaningful
@ -669,14 +670,14 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
cvm::error("Error: \"extendedFluctuation\" must be positive.\n", COLVARS_INPUT_ERROR);
return COLVARS_INPUT_ERROR;
}
ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
ext_force_k = proxy->boltzmann() * temp / (tolerance * tolerance);
cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " [E]/U^2\n");
get_keyval(conf, "extendedTimeConstant", extended_period, 200.0);
if (extended_period <= 0.0) {
cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", COLVARS_INPUT_ERROR);
}
ext_mass = (cvm::boltzmann() * temp * extended_period * extended_period)
ext_mass = (proxy->boltzmann() * temp * extended_period * extended_period)
/ (4.0 * PI * PI * tolerance * tolerance);
cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " [E]/(U/fs)^2 (U: colvar unit)\n");
}
@ -697,7 +698,7 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
enable(f_cv_Langevin);
ext_gamma *= 1.0e-3; // correct as long as input is required in ps-1 and cvm::dt() is in fs
// Adjust Langevin sigma for slow time step if time_step_factor != 1
ext_sigma = cvm::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor)));
ext_sigma = cvm::sqrt(2.0 * proxy->boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor)));
}
get_keyval_feature(this, conf, "reflectingLowerBoundary", f_cv_reflecting_lower_boundary, false);
@ -1664,6 +1665,7 @@ int colvar::calc_cvc_Jacobians(int first_cvc, size_t num_cvcs)
int colvar::collect_cvc_Jacobians()
{
colvarproxy *proxy = cvm::main()->proxy;
if (is_enabled(f_cv_Jacobian)) {
fj.reset();
for (size_t i = 0; i < cvcs.size(); i++) {
@ -1676,7 +1678,7 @@ int colvar::collect_cvc_Jacobians()
// linear combination is assumed
fj += (cvcs[i])->Jacobian_derivative() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
}
fj *= cvm::boltzmann() * cvm::temperature();
fj *= proxy->boltzmann() * proxy->target_temperature();
}
return COLVARS_OK;
@ -2411,8 +2413,8 @@ std::ostream & colvar::write_state(std::ostream &os) {
os << "}\n\n";
if (runave_os) {
cvm::main()->proxy->flush_output_stream(runave_os);
if (runave_outfile.size() > 0) {
cvm::main()->proxy->flush_output_stream(runave_outfile);
}
return os;
@ -2536,9 +2538,13 @@ int colvar::write_output_files()
}
cvm::log("Writing correlation function to file \""+acf_outfile+"\".\n");
cvm::backup_file(acf_outfile.c_str());
std::ostream *acf_os = cvm::proxy->output_stream(acf_outfile);
if (!acf_os) return cvm::get_error();
error_code |= write_acf(*acf_os);
std::ostream &acf_os = cvm::proxy->output_stream(acf_outfile,
"colvar ACF file");
if (!acf_os) {
error_code |= COLVARS_FILE_ERROR;
} else {
error_code |= write_acf(acf_os);
}
cvm::proxy->close_output_stream(acf_outfile);
}
}
@ -2807,6 +2813,7 @@ int colvar::write_acf(std::ostream &os)
int colvar::calc_runave()
{
int error_code = COLVARS_OK;
colvarproxy *proxy = cvm::main()->proxy;
if (x_history.empty()) {
@ -2831,17 +2838,17 @@ int colvar::calc_runave()
if ((*x_history_p).size() >= runave_length-1) {
if (runave_os == NULL) {
if (runave_outfile.size() == 0) {
runave_outfile = std::string(cvm::output_prefix()+"."+
this->name+".runave.traj");
}
if (! proxy->output_stream_exists(runave_outfile)) {
size_t const this_cv_width = x.output_width(cvm::cv_width);
cvm::proxy->backup_file(runave_outfile);
runave_os = cvm::proxy->output_stream(runave_outfile);
runave_os->setf(std::ios::scientific, std::ios::floatfield);
*runave_os << "# " << cvm::wrap_string("step", cvm::it_width-2)
std::ostream &runave_os = proxy->output_stream(runave_outfile,
"colvar running average");
runave_os.setf(std::ios::scientific, std::ios::floatfield);
runave_os << "# " << cvm::wrap_string("step", cvm::it_width-2)
<< " "
<< cvm::wrap_string("running average", this_cv_width)
<< " "
@ -2866,13 +2873,18 @@ int colvar::calc_runave()
}
runave_variance *= 1.0 / cvm::real(runave_length-1);
*runave_os << std::setw(cvm::it_width) << cvm::step_relative()
if (runave_outfile.size() > 0) {
std::ostream &runave_os = proxy->output_stream(runave_outfile);
runave_os << std::setw(cvm::it_width) << cvm::step_relative()
<< " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< runave << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< cvm::sqrt(runave_variance) << "\n";
}
}
history_add_value(runave_length, *x_history_p, x);
}

2
lib/colvars/colvar.h
View File

@ -551,8 +551,6 @@ protected:
size_t runave_stride;
/// Name of the file to write the running average
std::string runave_outfile;
/// File to write the running average
std::ostream *runave_os;
/// Current value of the running average
colvarvalue runave;
/// Current value of the square deviation from the running average

91
lib/colvars/colvar_UIestimator.h
View File

@ -1,4 +1,4 @@
// -*- c++ -*-
// -*- Mode:c++; c-basic-offset: 4; -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
@ -21,6 +21,7 @@
// only for colvar module!
// when integrated into other code, just remove this line and "...cvm::backup_file(...)"
#include "colvarmodule.h"
#include "colvarproxy.h"
namespace UIestimator {
const int Y_SIZE = 21; // defines the range of extended CV with respect to a given CV
@ -380,6 +381,8 @@ namespace UIestimator {
public:
// calculate gradients from the internal variables
void calc_pmf() {
colvarproxy *proxy = cvm::main()->proxy;
int norm;
int i, j, k;
@ -455,7 +458,7 @@ namespace UIestimator {
std::vector<double> grad_temp(dimension, 0);
for (k = 0; k < dimension; k++) {
diff_av[k] /= (norm > 0 ? norm : 1);
av[k] = cvm::boltzmann() * temperature * av[k] / (norm > 0 ? norm : 1);
av[k] = proxy->boltzmann() * temperature * av[k] / (norm > 0 ? norm : 1);
grad_temp[k] = av[k] - krestr[k] * diff_av[k];
}
grad.set_value(loop_flag_x, grad_temp);
@ -515,15 +518,16 @@ namespace UIestimator {
// only for colvars module!
if (written_1D) cvm::backup_file(pmf_filename.c_str());
std::ostream* ofile_pmf = cvm::proxy->output_stream(pmf_filename.c_str());
std::ostream &ofile_pmf = cvm::proxy->output_stream(pmf_filename,
"PMF file");
std::vector<double> position(1, 0);
for (double i = lowerboundary[0]; i < upperboundary[0] + EPSILON; i += width[0]) {
*ofile_pmf << i << " ";
ofile_pmf << i << " ";
position[0] = i + EPSILON;
*ofile_pmf << oneD_pmf.get_value(position) << std::endl;
ofile_pmf << oneD_pmf.get_value(position) << std::endl;
}
cvm::proxy->close_output_stream(pmf_filename.c_str());
cvm::proxy->close_output_stream(pmf_filename);
written_1D = true;
}
@ -541,7 +545,8 @@ namespace UIestimator {
void write_interal_data() {
std::string internal_filename = output_filename + ".UI.internal";
std::ostream* ofile_internal = cvm::proxy->output_stream(internal_filename.c_str());
std::ostream &ofile_internal = cvm::proxy->output_stream(internal_filename,
"UI internal file");
std::vector<double> loop_flag(dimension, 0);
for (int i = 0; i < dimension; i++) {
@ -551,11 +556,11 @@ namespace UIestimator {
int n = 0;
while (n >= 0) {
for (int j = 0; j < dimension; j++) {
*ofile_internal << loop_flag[j] + 0.5 * width[j] << " ";
ofile_internal << loop_flag[j] + 0.5 * width[j] << " ";
}
for (int k = 0; k < dimension; k++) {
*ofile_internal << grad.get_value(loop_flag)[k] << " ";
ofile_internal << grad.get_value(loop_flag)[k] << " ";
}
std::vector<double> ii(dimension,0);
@ -563,10 +568,10 @@ namespace UIestimator {
for (double j = loop_flag[1] - 10; j< loop_flag[1] + 10 + EPSILON; j+=width[1]) {
ii[0] = i;
ii[1] = j;
*ofile_internal << i <<" "<<j<<" "<< distribution_x_y.get_value(loop_flag,ii)<< " ";
ofile_internal << i <<" "<<j<<" "<< distribution_x_y.get_value(loop_flag,ii)<< " ";
}
}
*ofile_internal << std::endl;
ofile_internal << std::endl;
// iterate over any dimensions
n = dimension - 1;
@ -596,13 +601,16 @@ namespace UIestimator {
//if (written) cvm::backup_file(hist_filename.c_str());
if (written) cvm::backup_file(count_filename.c_str());
std::ostream* ofile = cvm::proxy->output_stream(grad_filename.c_str());
std::ostream* ofile_hist = cvm::proxy->output_stream(hist_filename.c_str(), std::ios::app);
std::ostream* ofile_count = cvm::proxy->output_stream(count_filename.c_str());
std::ostream &ofile = cvm::proxy->output_stream(grad_filename,
"gradient file");
std::ostream &ofile_hist = cvm::proxy->output_stream(hist_filename,
"gradient history file");
std::ostream &ofile_count = cvm::proxy->output_stream(count_filename,
"count file");
writehead(*ofile);
writehead(*ofile_hist);
writehead(*ofile_count);
writehead(ofile);
writehead(ofile_hist);
writehead(ofile_count);
if (dimension == 1) {
calc_1D_pmf();
@ -617,19 +625,19 @@ namespace UIestimator {
i = 0;
while (i >= 0) {
for (j = 0; j < dimension; j++) {
*ofile << loop_flag[j] + 0.5 * width[j] << " ";
*ofile_hist << loop_flag[j] + 0.5 * width[j] << " ";
*ofile_count << loop_flag[j] + 0.5 * width[j] << " ";
ofile << loop_flag[j] + 0.5 * width[j] << " ";
ofile_hist << loop_flag[j] + 0.5 * width[j] << " ";
ofile_count << loop_flag[j] + 0.5 * width[j] << " ";
}
if (restart == false) {
for (j = 0; j < dimension; j++) {
*ofile << grad.get_value(loop_flag)[j] << " ";
*ofile_hist << grad.get_value(loop_flag)[j] << " ";
ofile << grad.get_value(loop_flag)[j] << " ";
ofile_hist << grad.get_value(loop_flag)[j] << " ";
}
*ofile << std::endl;
*ofile_hist << std::endl;
*ofile_count << count.get_value(loop_flag) << " " <<std::endl;
ofile << std::endl;
ofile_hist << std::endl;
ofile_count << count.get_value(loop_flag) << " " <<std::endl;
}
else {
double final_grad = 0;
@ -639,12 +647,12 @@ namespace UIestimator {
final_grad = grad.get_value(loop_flag)[j];
else
final_grad = ((grad.get_value(loop_flag)[j] * count.get_value(loop_flag) + input_grad.get_value(loop_flag)[j] * input_count.get_value(loop_flag)) / total_count_temp);
*ofile << final_grad << " ";
*ofile_hist << final_grad << " ";
ofile << final_grad << " ";
ofile_hist << final_grad << " ";
}
*ofile << std::endl;
*ofile_hist << std::endl;
*ofile_count << (count.get_value(loop_flag) + input_count.get_value(loop_flag)) << " " <<std::endl;
ofile << std::endl;
ofile_hist << std::endl;
ofile_count << (count.get_value(loop_flag) + input_count.get_value(loop_flag)) << " " <<std::endl;
}
// iterate over any dimensions
@ -654,16 +662,16 @@ namespace UIestimator {
if (loop_flag[i] > upperboundary[i] - width[i] + EPSILON) {
loop_flag[i] = lowerboundary[i];
i--;
*ofile << std::endl;
*ofile_hist << std::endl;
*ofile_count << std::endl;
ofile << std::endl;
ofile_hist << std::endl;
ofile_count << std::endl;
}
else
break;
}
}
cvm::proxy->close_output_stream(grad_filename.c_str());
cvm::proxy->close_output_stream(hist_filename.c_str());
// cvm::proxy->close_output_stream(hist_filename.c_str());
cvm::proxy->close_output_stream(count_filename.c_str());
written = true;
@ -677,6 +685,7 @@ namespace UIestimator {
int dimension_temp;
int i, j, k, l, m;
colvarproxy *proxy = cvm::main()->proxy;
std::vector<double> loop_bin_size(dimension, 0);
std::vector<double> position_temp(dimension, 0);
std::vector<double> grad_temp(dimension, 0);
@ -687,8 +696,14 @@ namespace UIestimator {
std::string count_filename = filename[i] + ".UI.count";
std::string grad_filename = filename[i] + ".UI.grad";
std::ifstream count_file(count_filename.c_str(), std::ios::in);
std::ifstream grad_file(grad_filename.c_str(), std::ios::in);
std::istream &count_file =
proxy->input_stream(count_filename, "count filename");
std::istream &grad_file =
proxy->input_stream(grad_filename, "gradient filename");
if (!count_file || !grad_file) {
return;
}
count_file >> sharp >> dimension_temp;
grad_file >> sharp >> dimension_temp;
@ -724,8 +739,8 @@ namespace UIestimator {
input_count.increase_value(position_temp, count_temp);
}
count_file.close();
grad_file.close();
proxy->close_input_stream(count_filename);
proxy->close_input_stream(grad_filename);
}
}
};

1
lib/colvars/colvar_arithmeticpath.h
View File

@ -5,7 +5,6 @@
#include <vector>
#include <cmath>
#include <iostream>
#include <limits>
#include <string>

2
lib/colvars/colvar_geometricpath.h
View File

@ -12,10 +12,8 @@
#include <vector>
#include <cmath>
#include <iostream>
#include <algorithm>
#include <string>
#include <map>
namespace GeometricPathCV {

32
lib/colvars/colvar_neuralnetworkcompute.cpp
View File

@ -1,6 +1,19 @@
// -*- Mode:c++; c-basic-offset: 4; -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <iostream>
#include <fstream>
#if (__cplusplus >= 201103L)
#include "colvar_neuralnetworkcompute.h"
#include "colvarparse.h"
#include "colvarproxy.h"
namespace neuralnetworkCV {
std::map<std::string, std::pair<std::function<double(double)>, std::function<double(double)>>> activation_function_map
@ -124,12 +137,10 @@ void denseLayer::readFromFile(const std::string& weights_file, const std::string
m_weights.clear();
m_biases.clear();
std::string line;
std::ifstream ifs_weights(weights_file.c_str());
if (!ifs_weights) {
throw std::runtime_error("Cannot open file " + weights_file);
}
colvarproxy *proxy = cvm::main()->proxy;
auto &ifs_weights = proxy->input_stream(weights_file, "weights file");
while (std::getline(ifs_weights, line)) {
if (ifs_weights.bad()) {
if (!ifs_weights) {
throw std::runtime_error("I/O error while reading " + weights_file);
}
std::vector<std::string> splitted_data;
@ -146,13 +157,12 @@ void denseLayer::readFromFile(const std::string& weights_file, const std::string
m_weights.push_back(weights_tmp);
}
}
proxy->close_input_stream(weights_file);
// parse biases file
std::ifstream ifs_biases(biases_file.c_str());
if (!ifs_biases) {
throw std::runtime_error("Cannot open file " + biases_file);
}
auto &ifs_biases = proxy->input_stream(biases_file, "biases file");
while (std::getline(ifs_biases, line)) {
if (ifs_biases.bad()) {
if (!ifs_biases) {
throw std::runtime_error("I/O error while reading " + biases_file);
}
std::vector<std::string> splitted_data;
@ -167,6 +177,8 @@ void denseLayer::readFromFile(const std::string& weights_file, const std::string
m_biases.push_back(bias);
}
}
proxy->close_input_stream(biases_file);
m_input_size = m_weights[0].size();
m_output_size = m_weights.size();
}

10
lib/colvars/colvar_neuralnetworkcompute.h
View File

@ -1,3 +1,12 @@
// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#if (__cplusplus >= 201103L)
#ifndef NEURALNETWORKCOMPUTE_H
#define NEURALNETWORKCOMPUTE_H
@ -5,7 +14,6 @@
#include <vector>
#include <functional>
#include <string>
#include <iostream>
#include <cmath>
#include <memory>
#include <map>

28
lib/colvars/colvaratoms.cpp
View File

@ -10,6 +10,8 @@
#include <list>
#include <vector>
#include <algorithm>
#include <sstream>
#include <iomanip>
#include "colvarmodule.h"
#include "colvarproxy.h"
@ -29,12 +31,8 @@ cvm::atom::atom()
cvm::atom::atom(int atom_number)
{
colvarproxy *p = cvm::proxy;
colvarproxy *p = cvm::main()->proxy;
index = p->init_atom(atom_number);
if (cvm::debug()) {
cvm::log("The index of this atom in the colvarproxy arrays is "+
cvm::to_str(index)+".\n");
}
id = p->get_atom_id(index);
update_mass();
update_charge();
@ -46,12 +44,8 @@ cvm::atom::atom(cvm::residue_id const &residue,
std::string const &atom_name,
std::string const &segment_id)
{
colvarproxy *p = cvm::proxy;
colvarproxy *p = cvm::main()->proxy;
index = p->init_atom(residue, atom_name, segment_id);
if (cvm::debug()) {
cvm::log("The index of this atom in the colvarproxy_namd arrays is "+
cvm::to_str(index)+".\n");
}
id = p->get_atom_id(index);
update_mass();
update_charge();
@ -62,7 +56,9 @@ cvm::atom::atom(cvm::residue_id const &residue,
cvm::atom::atom(atom const &a)
: index(a.index)
{
id = (cvm::proxy)->get_atom_id(index);
colvarproxy *p = cvm::main()->proxy;
id = p->get_atom_id(index);
p->increase_refcount(index);
update_mass();
update_charge();
reset_data();
@ -72,7 +68,7 @@ cvm::atom::atom(atom const &a)
cvm::atom::~atom()
{
if (index >= 0) {
(cvm::proxy)->clear_atom(index);
(cvm::main()->proxy)->clear_atom(index);
}
}
@ -80,7 +76,7 @@ cvm::atom::~atom()
cvm::atom & cvm::atom::operator = (cvm::atom const &a)
{
index = a.index;
id = (cvm::proxy)->get_atom_id(index);
id = (cvm::main()->proxy)->get_atom_id(index);
update_mass();
update_charge();
reset_data();
@ -113,7 +109,7 @@ cvm::atom_group::atom_group(std::vector<cvm::atom> const &atoms_in)
cvm::atom_group::~atom_group()
{
if (is_enabled(f_ag_scalable) && !b_dummy) {
(cvm::proxy)->clear_atom_group(index);
(cvm::main()->proxy)->clear_atom_group(index);
index = -1;
}
@ -330,7 +326,7 @@ void cvm::atom_group::update_total_mass()
}
if (is_enabled(f_ag_scalable)) {
total_mass = (cvm::proxy)->get_atom_group_mass(index);
total_mass = (cvm::main()->proxy)->get_atom_group_mass(index);
} else {
total_mass = 0.0;
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
@ -351,7 +347,7 @@ void cvm::atom_group::update_total_charge()
}
if (is_enabled(f_ag_scalable)) {
total_charge = (cvm::proxy)->get_atom_group_charge(index);
total_charge = (cvm::main()->proxy)->get_atom_group_charge(index);
} else {
total_charge = 0.0;
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {

94
lib/colvars/colvarbias.cpp
View File

@ -7,7 +7,7 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <fstream>
#include <iostream>
#include <cstring>
#include "colvarmodule.h"
@ -42,6 +42,8 @@ colvarbias::colvarbias(char const *key)
int colvarbias::init(std::string const &conf)
{
int error_code = COLVARS_OK;
name = bias_type + cvm::to_str(rank);
colvarparse::set_string(conf);
@ -59,9 +61,9 @@ int colvarbias::init(std::string const &conf)
if (bias_with_name != NULL) {
if ((bias_with_name->rank != this->rank) ||
(bias_with_name->bias_type != this->bias_type)) {
cvm::error("Error: this bias cannot have the same name, \""+this->name+
"\", as another bias.\n", COLVARS_INPUT_ERROR);
return COLVARS_INPUT_ERROR;
error_code |= cvm::error("Error: this bias cannot have the same name, \""+
this->name+"\", as another bias.\n",
COLVARS_INPUT_ERROR);
}
}
description = "bias " + name;
@ -71,9 +73,9 @@ int colvarbias::init(std::string const &conf)
std::vector<std::string> colvar_names;
if (get_keyval(conf, "colvars", colvar_names)) {
if (num_variables()) {
cvm::error("Error: cannot redefine the colvars that a bias was already defined on.\n",
error_code |= cvm::error("Error: cannot redefine the colvars that "
"a bias was already defined on.\n",
COLVARS_INPUT_ERROR);
return COLVARS_INPUT_ERROR;
}
for (i = 0; i < colvar_names.size(); i++) {
add_colvar(colvar_names[i]);
@ -82,8 +84,8 @@ int colvarbias::init(std::string const &conf)
}
if (!num_variables()) {
cvm::error("Error: no collective variables specified.\n", COLVARS_INPUT_ERROR);
return COLVARS_INPUT_ERROR;
error_code |= cvm::error("Error: no collective variables specified.\n",
COLVARS_INPUT_ERROR);
}
} else {
@ -112,8 +114,8 @@ int colvarbias::init(std::string const &conf)
get_keyval(conf, "timeStepFactor", time_step_factor, time_step_factor);
if (time_step_factor < 1) {
cvm::error("Error: timeStepFactor must be 1 or greater.\n");
return COLVARS_ERROR;
error_code |= cvm::error("Error: timeStepFactor must be 1 or greater.\n",
COLVARS_INPUT_ERROR);
}
// Use the scaling factors from a grid?
@ -124,25 +126,17 @@ int colvarbias::init(std::string const &conf)
std::string biasing_force_scaling_factors_in_filename;
get_keyval(conf, "scaledBiasingForceFactorsGrid",
biasing_force_scaling_factors_in_filename, std::string());
std::ifstream is;
cvm::log("Reading scaling factors for the forces of bias " +
name + " from " + biasing_force_scaling_factors_in_filename);
is.open(biasing_force_scaling_factors_in_filename.c_str());
if (!is.is_open()) {
cvm::error("Error opening the grid file " +
biasing_force_scaling_factors_in_filename + " for reading");
}
biasing_force_scaling_factors = new colvar_grid_scalar(colvars);
biasing_force_scaling_factors->read_multicol(is, true);
error_code |= biasing_force_scaling_factors->read_multicol(biasing_force_scaling_factors_in_filename,
"grid file");
biasing_force_scaling_factors_bin.assign(num_variables(), 0);
is.close();
}
// Now that children are defined, we can solve dependencies
enable(f_cvb_active);
if (cvm::debug()) print_state();
return COLVARS_OK;
return error_code;
}
@ -377,10 +371,11 @@ int colvarbias::calc_forces(std::vector<colvarvalue> const *)
}
void colvarbias::communicate_forces()
int colvarbias::communicate_forces()
{
int error_code = COLVARS_OK;
if (! is_enabled(f_cvb_apply_force)) {
return;
return error_code;
}
cvm::real biasing_force_factor = 1.0;
size_t i = 0;
@ -409,6 +404,7 @@ void colvarbias::communicate_forces()
}
previous_colvar_forces[i] = colvar_forces[i];
}
return error_code;
}
@ -573,11 +569,11 @@ int colvarbias::write_state_prefix(std::string const &prefix)
{
std::string const filename =
cvm::state_file_prefix(prefix.c_str())+".colvars.state";
std::ostream *os = cvm::proxy->output_stream(filename.c_str());
std::ostream &os = cvm::proxy->output_stream(filename.c_str(), "bias state file");
int error_code = COLVARS_OK;
if (os != NULL) {
os->setf(std::ios::scientific, std::ios::floatfield);
error_code = write_state(*os).good() ? COLVARS_OK : COLVARS_FILE_ERROR;
if (os) {
os.setf(std::ios::scientific, std::ios::floatfield);
error_code = write_state(os) ? COLVARS_OK : COLVARS_FILE_ERROR;
} else {
error_code = COLVARS_FILE_ERROR;
}
@ -600,17 +596,19 @@ int colvarbias::write_state_string(std::string &output)
int colvarbias::read_state_prefix(std::string const &prefix)
{
std::string filename((prefix+std::string(".colvars.state")).c_str());
std::ifstream is(filename.c_str());
if (!is.good()) {
// try without the suffix
is.clear();
std::string filename(prefix+std::string(".colvars.state"));
std::istream *is = &(cvm::main()->proxy->input_stream(filename,
"bias state file",
false));
if (!*is) {
filename = prefix;
is.open(filename.c_str());
is = &(cvm::main()->proxy->input_stream(filename, "bias state file"));
}
return read_state(is).good() ? COLVARS_OK :
cvm::error("Error: in reading state for \""+name+"\" from input file \""+
std::string(filename)+"\".\n", COLVARS_FILE_ERROR);
if (read_state(*is)) {
return cvm::main()->proxy->close_input_stream(filename);
}
return COLVARS_FILE_ERROR;
}
@ -899,6 +897,8 @@ std::istream & colvarbias_ti::read_state_data(std::istream &is)
int colvarbias_ti::write_output_files()
{
int error_code = COLVARS_OK;
if (!has_data) {
// nothing to write
return COLVARS_OK;
@ -906,38 +906,30 @@ int colvarbias_ti::write_output_files()
std::string const ti_output_prefix = cvm::output_prefix()+"."+this->name;
std::ostream *os = NULL;
if (is_enabled(f_cvb_write_ti_samples)) {
std::string const ti_count_file_name(ti_output_prefix+".ti.count");
os = cvm::proxy->output_stream(ti_count_file_name);
if (os) {
ti_count->write_multicol(*os);
cvm::proxy->close_output_stream(ti_count_file_name);
}
error_code |= ti_count->write_multicol(ti_count_file_name, "TI count file");
std::string const ti_grad_file_name(ti_output_prefix+".ti.force");
os = cvm::proxy->output_stream(ti_grad_file_name);
if (os) {
ti_avg_forces->write_multicol(*os);
cvm::proxy->close_output_stream(ti_grad_file_name);
}
error_code |= ti_avg_forces->write_multicol(ti_grad_file_name, "TI gradient file");
}
if (is_enabled(f_cvb_write_ti_pmf)) {
std::string const pmf_file_name(ti_output_prefix+".ti.pmf");
cvm::log("Writing TI PMF to file \""+pmf_file_name+"\".\n");
os = cvm::proxy->output_stream(pmf_file_name);
std::ostream &os = cvm::proxy->output_stream(pmf_file_name, "TI PMF");
if (os) {
// get the FE gradient
ti_avg_forces->multiply_constant(-1.0);
ti_avg_forces->write_1D_integral(*os);
ti_avg_forces->write_1D_integral(os);
ti_avg_forces->multiply_constant(-1.0);
cvm::proxy->close_output_stream(pmf_file_name);
} else {
error_code |= COLVARS_FILE_ERROR;
}
}
return COLVARS_OK;
return error_code;
}

2
lib/colvars/colvarbias.h
View File

@ -73,7 +73,7 @@ public:
virtual int calc_forces(std::vector<colvarvalue> const *values);
/// Send forces to the collective variables
void communicate_forces();
int communicate_forces();
/// Carry out operations needed before next step is run
virtual int end_of_step();

77
lib/colvars/colvarbias_abf.cpp
View File

@ -7,6 +7,8 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <iostream>
#include "colvarmodule.h"
#include "colvar.h"
#include "colvarbias_abf.h"
@ -38,17 +40,17 @@ colvarbias_abf::colvarbias_abf(char const *key)
int colvarbias_abf::init(std::string const &conf)
{
colvarproxy *proxy = cvm::main()->proxy;
colvarbias::init(conf);
cvm::main()->cite_feature("ABF colvar bias implementation");
colvarproxy *proxy = cvm::main()->proxy;
enable(f_cvb_scalar_variables);
enable(f_cvb_calc_pmf);
// TODO relax this in case of VMD plugin
if (cvm::temperature() == 0.0)
if ((proxy->target_temperature() == 0.0) && proxy->simulation_running()) {
cvm::log("WARNING: ABF should not be run without a thermostat or at 0 Kelvin!\n");
}
// ************* parsing general ABF options ***********************
@ -277,7 +279,7 @@ int colvarbias_abf::init(std::string const &conf)
cvm::restart_out_freq,
UI_restart, // whether restart from a .count and a .grad file
input_prefix, // the prefixes of input files
cvm::temperature());
proxy->target_temperature());
}
}
@ -599,17 +601,17 @@ int colvarbias_abf::replica_share() {
template <class T> int colvarbias_abf::write_grid_to_file(T const *grid,
std::string const &filename,
bool close) {
std::ostream *os = cvm::proxy->output_stream(filename);
std::ostream &os = cvm::proxy->output_stream(filename);
if (!os) {
return cvm::error("Error opening file " + filename + " for writing.\n", COLVARS_ERROR | COLVARS_FILE_ERROR);
}
grid->write_multicol(*os);
grid->write_multicol(os);
if (close) {
cvm::proxy->close_output_stream(filename);
} else {
// Insert empty line between frames in history files
*os << std::endl;
cvm::proxy->flush_output_stream(os);
os << std::endl;
cvm::proxy->flush_output_stream(filename);
}
// In dimension higher than 2, dx is easier to handle and visualize
@ -617,11 +619,11 @@ template <class T> int colvarbias_abf::write_grid_to_file(T const *grid,
// (could be implemented as multiple dx files)
if (num_variables() > 2 && close) {
std::string dx = filename + ".dx";
std::ostream *dx_os = cvm::proxy->output_stream(dx);
std::ostream &dx_os = cvm::proxy->output_stream(dx);
if (!dx_os) {
return cvm::error("Error opening file " + dx + " for writing.\n", COLVARS_ERROR | COLVARS_FILE_ERROR);
}
grid->write_opendx(*dx_os);
grid->write_opendx(dx_os);
// if (close) {
cvm::proxy->close_output_stream(dx);
// }
@ -637,6 +639,8 @@ template <class T> int colvarbias_abf::write_grid_to_file(T const *grid,
void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool close)
{
colvarproxy *proxy = cvm::main()->proxy;
write_grid_to_file<colvar_grid_count>(samples, prefix + ".count", close);
write_grid_to_file<colvar_grid_gradient>(gradients, prefix + ".grad", close);
@ -660,7 +664,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool clo
czar_gradients->index_ok(ix); czar_gradients->incr(ix)) {
for (size_t n = 0; n < czar_gradients->multiplicity(); n++) {
czar_gradients->set_value(ix, z_gradients->value_output(ix, n)
- cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n), n);
- proxy->target_temperature() * proxy->boltzmann() * z_samples->log_gradient_finite_diff(ix, n), n);
}
}
write_grid_to_file<colvar_grid_gradient>(czar_gradients, prefix + ".czar.grad", close);
@ -698,8 +702,10 @@ int colvarbias_abf::bin_count(int bin_index) {
}
void colvarbias_abf::read_gradients_samples()
int colvarbias_abf::read_gradients_samples()
{
int error_code = COLVARS_OK;
std::string samples_in_name, gradients_in_name, z_samples_in_name, z_gradients_in_name;
for ( size_t i = 0; i < input_prefix.size(); i++ ) {
@ -708,43 +714,30 @@ void colvarbias_abf::read_gradients_samples()
z_samples_in_name = input_prefix[i] + ".zcount";
z_gradients_in_name = input_prefix[i] + ".zgrad";
// For user-provided files, the per-bias naming scheme may not apply
cvm::log("Reading sample count from " + samples_in_name +
" and gradient from " + gradients_in_name);
std::ifstream is;
error_code |= samples->read_multicol(samples_in_name,
"ABF samples file",
true);
cvm::log("Reading sample count from " + samples_in_name + " and gradient from " + gradients_in_name);
is.open(samples_in_name.c_str());
if (!is.is_open()) 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.is_open()) {
cvm::error("Error opening ABF gradient file " +
gradients_in_name + " for reading", COLVARS_INPUT_ERROR);
} else {
gradients->read_multicol(is, true);
is.close();
}
error_code |= gradients->read_multicol(gradients_in_name,
"ABF gradient file",
true);
if (b_CZAR_estimator) {
// Read eABF z-averaged data for CZAR
cvm::log("Reading z-histogram from " + z_samples_in_name + " and z-gradient from " + z_gradients_in_name);
is.clear();
is.open(z_samples_in_name.c_str());
if (!is.is_open()) cvm::error("Error opening eABF z-histogram file " + z_samples_in_name + " for reading");
z_samples->read_multicol(is, true);
is.close();
is.clear();
is.open(z_gradients_in_name.c_str());
if (!is.is_open()) cvm::error("Error opening eABF z-gradient file " + z_gradients_in_name + " for reading");
z_gradients->read_multicol(is, true);
is.close();
error_code |= z_samples->read_multicol(z_samples_in_name,
"eABF z-histogram file",
true);
error_code |= z_gradients->read_multicol(z_gradients_in_name,
"eABF z-gradient file",
true);
}
}
return;
return error_code;
}

2
lib/colvars/colvarbias_abf.h
View File

@ -155,7 +155,7 @@ private:
void write_gradients_samples(const std::string &prefix, bool close = true);
/// Read human-readable FE gradients and sample count (if not using restart)
void read_gradients_samples();
int read_gradients_samples();
/// Template used in write_gradient_samples()
template <class T> int write_grid_to_file(T const *grid,

24
lib/colvars/colvarbias_alb.cpp
View File

@ -7,9 +7,12 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <iostream>
#include <iomanip>
#include <cstdlib>
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "colvarbias.h"
#include "colvarbias_alb.h"
@ -36,6 +39,7 @@ colvarbias_alb::colvarbias_alb(char const *key)
int colvarbias_alb::init(std::string const &conf)
{
colvarproxy *proxy = cvm::main()->proxy;
colvarbias::init(conf);
cvm::main()->cite_feature("ALB colvar bias implementation");
@ -110,10 +114,12 @@ int colvarbias_alb::init(std::string const &conf)
if (!get_keyval(conf, "forceRange", max_coupling_range, max_coupling_range)) {
//set to default
for (i = 0; i < num_variables(); i++) {
if (cvm::temperature() > 0)
max_coupling_range[i] = 3 * cvm::temperature() * cvm::boltzmann();
else
max_coupling_range[i] = 3 * cvm::boltzmann();
if (proxy->target_temperature() > 0.0) {
max_coupling_range[i] = 3 * proxy->target_temperature() *
proxy->boltzmann();
} else {
max_coupling_range[i] = 3 * proxy->boltzmann();
}
}
}
@ -139,6 +145,7 @@ colvarbias_alb::~colvarbias_alb()
int colvarbias_alb::update()
{
colvarproxy *proxy = cvm::main()->proxy;
bias_energy = 0.0;
update_calls++;
@ -214,10 +221,11 @@ int colvarbias_alb::update()
temp = 2. * (means[i] / (static_cast<cvm::real> (colvar_centers[i])) - 1) * ssd[i] / (update_calls - 1);
if (cvm::temperature() > 0)
step_size = temp / (cvm::temperature() * cvm::boltzmann());
else
step_size = temp / cvm::boltzmann();
if (proxy->target_temperature() > 0.0) {
step_size = temp / (proxy->target_temperature() * proxy->boltzmann());
} else {
step_size = temp / proxy->boltzmann();
}
means[i] = 0;
ssd[i] = 0;

22
lib/colvars/colvarbias_histogram.cpp
View File

@ -179,31 +179,19 @@ int colvarbias_histogram::write_output_files()
return COLVARS_OK;
}
int error_code = COLVARS_OK;
if (out_name.size() && out_name != "none") {
cvm::log("Writing the histogram file \""+out_name+"\".\n");
cvm::backup_file(out_name.c_str());
std::ostream *grid_os = cvm::proxy->output_stream(out_name);
if (!grid_os) {
return cvm::error("Error opening histogram file "+out_name+
" for writing.\n", COLVARS_FILE_ERROR);
}
grid->write_multicol(*grid_os);
cvm::proxy->close_output_stream(out_name);
error_code |= grid->write_multicol(out_name, "histogram output file");
}
if (out_name_dx.size() && out_name_dx != "none") {
cvm::log("Writing the histogram file \""+out_name_dx+"\".\n");
cvm::backup_file(out_name_dx.c_str());
std::ostream *grid_os = cvm::proxy->output_stream(out_name_dx);
if (!grid_os) {
return cvm::error("Error opening histogram file "+out_name_dx+
" for writing.\n", COLVARS_FILE_ERROR);
}
grid->write_opendx(*grid_os);
cvm::proxy->close_output_stream(out_name_dx);
error_code |= grid->write_opendx(out_name_dx, "histogram DX output file");
}
return COLVARS_OK;
return error_code;
}

94
lib/colvars/colvarbias_histogram_reweight_amd.cpp
View File

@ -81,6 +81,7 @@ int colvarbias_reweightaMD::init(std::string const &conf) {
}
int colvarbias_reweightaMD::update() {
colvarproxy *proxy = cvm::main()->proxy;
int error_code = COLVARS_OK;
if (cvm::step_relative() >= start_after_steps) {
// update base class
@ -110,7 +111,7 @@ int colvarbias_reweightaMD::update() {
grid->acc_value(previous_bin, reweighting_factor);
if (b_use_cumulant_expansion) {
const cvm::real dV = cvm::logn(reweighting_factor) *
cvm::temperature() * cvm::boltzmann();
proxy->target_temperature() * proxy->boltzmann();
grid_dV->acc_value(previous_bin, dV);
grid_dV_square->acc_value(previous_bin, dV * dV);
}
@ -129,7 +130,7 @@ int colvarbias_reweightaMD::update() {
grid->acc_value(previous_bin, reweighting_factor);
if (b_use_cumulant_expansion) {
const cvm::real dV = cvm::logn(reweighting_factor) *
cvm::temperature() * cvm::boltzmann();
proxy->target_temperature() * proxy->boltzmann();
grid_dV->acc_value(previous_bin, dV);
grid_dV_square->acc_value(previous_bin, dV * dV);
}
@ -138,10 +139,6 @@ int colvarbias_reweightaMD::update() {
}
previous_bin.assign(num_variables(), 0);
if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
write_output_files();
}
error_code |= cvm::get_error();
}
return error_code;
@ -160,7 +157,7 @@ int colvarbias_reweightaMD::write_output_files() {
(cvm::step_absolute() % history_freq) == 0;
if (write_history) {
error_code |= write_exponential_reweighted_pmf(
out_name_pmf + ".hist", (cvm::step_relative() > 0));
out_name_pmf + ".hist", true);
error_code |= write_count(out_count_prefix + ".hist",
(cvm::step_relative() > 0));
}
@ -170,7 +167,7 @@ int colvarbias_reweightaMD::write_output_files() {
error_code |= write_cumulant_expansion_pmf(out_name_cumulant_pmf);
if (write_history) {
error_code |= write_cumulant_expansion_pmf(
out_name_cumulant_pmf + ".hist", (cvm::step_relative() > 0));
out_name_cumulant_pmf + ".hist", true);
}
}
error_code |= cvm::get_error();
@ -178,17 +175,13 @@ int colvarbias_reweightaMD::write_output_files() {
}
int colvarbias_reweightaMD::write_exponential_reweighted_pmf(
const std::string& p_output_prefix, bool append) {
const std::string& p_output_prefix, bool keep_open) {
const std::string output_pmf = p_output_prefix + ".pmf";
cvm::log("Writing the accelerated MD PMF file \"" + output_pmf + "\".\n");
if (!append) {
cvm::backup_file(output_pmf.c_str());
}
const std::ios::openmode mode = (append ? std::ios::app : std::ios::out);
std::ostream *pmf_grid_os = cvm::proxy->output_stream(output_pmf, mode);
std::ostream &pmf_grid_os = cvm::proxy->output_stream(output_pmf, "PMF file");
if (!pmf_grid_os) {
return cvm::error("Error opening PMF file " + output_pmf +
" for writing.\n", COLVARS_FILE_ERROR);
return COLVARS_FILE_ERROR;
}
pmf_grid_exp_avg->copy_grid(*grid);
// compute the average
@ -200,19 +193,18 @@ int colvarbias_reweightaMD::write_exponential_reweighted_pmf(
}
}
hist_to_pmf(pmf_grid_exp_avg, grid_count);
pmf_grid_exp_avg->write_multicol(*pmf_grid_os);
pmf_grid_exp_avg->write_multicol(pmf_grid_os);
if (!keep_open) {
cvm::proxy->close_output_stream(output_pmf);
}
if (b_write_gradients) {
const std::string output_grad = p_output_prefix + ".grad";
cvm::log("Writing the accelerated MD gradients file \"" + output_grad +
"\".\n");
if (!append) {
cvm::backup_file(output_grad.c_str());
}
std::ostream *grad_grid_os = cvm::proxy->output_stream(output_grad, mode);
std::ostream &grad_grid_os = cvm::proxy->output_stream(output_grad, "gradient file");
if (!grad_grid_os) {
return cvm::error("Error opening grad file " + output_grad +
" for writing.\n", COLVARS_FILE_ERROR);
return COLVARS_FILE_ERROR;
}
for (std::vector<int> ix = grad_grid_exp_avg->new_index();
grad_grid_exp_avg->index_ok(ix); grad_grid_exp_avg->incr(ix)) {
@ -221,38 +213,37 @@ int colvarbias_reweightaMD::write_exponential_reweighted_pmf(
ix, pmf_grid_exp_avg->gradient_finite_diff(ix, n), n);
}
}
grad_grid_exp_avg->write_multicol(*grad_grid_os);
grad_grid_exp_avg->write_multicol(grad_grid_os);
if (!keep_open) {
cvm::proxy->close_output_stream(output_grad);
}
}
return COLVARS_OK;
}
int colvarbias_reweightaMD::write_cumulant_expansion_pmf(
const std::string& p_output_prefix, bool append) {
const std::string& p_output_prefix, bool keep_open) {
const std::string output_pmf = p_output_prefix + ".pmf";
cvm::log("Writing the accelerated MD PMF file using cumulant expansion: \"" + output_pmf + "\".\n");
if (!append) cvm::backup_file(output_pmf.c_str());
const std::ios::openmode mode = (append ? std::ios::app : std::ios::out);
std::ostream *pmf_grid_cumulant_os = cvm::proxy->output_stream(output_pmf, mode);
std::ostream &pmf_grid_cumulant_os = cvm::proxy->output_stream(output_pmf, "PMF file");
if (!pmf_grid_cumulant_os) {
return cvm::error("Error opening PMF file " + output_pmf +
" for writing.\n", COLVARS_FILE_ERROR);
return COLVARS_FILE_ERROR;
}
compute_cumulant_expansion_factor(grid_dV, grid_dV_square,
grid_count, pmf_grid_cumulant);
hist_to_pmf(pmf_grid_cumulant, grid_count);
pmf_grid_cumulant->write_multicol(*pmf_grid_cumulant_os);
pmf_grid_cumulant->write_multicol(pmf_grid_cumulant_os);
if (!keep_open) {
cvm::proxy->close_output_stream(output_pmf);
}
if (b_write_gradients) {
const std::string output_grad = p_output_prefix + ".grad";
cvm::log("Writing the accelerated MD gradients file \"" + output_grad + "\".\n");
if (!append) {
cvm::backup_file(output_grad.c_str());
}
std::ostream *grad_grid_os = cvm::proxy->output_stream(output_grad, mode);
std::ostream &grad_grid_os = cvm::proxy->output_stream(output_grad, "grad file");
if (!grad_grid_os) {
return cvm::error("Error opening grad file " + output_grad +
" for writing.\n", COLVARS_FILE_ERROR);
return COLVARS_FILE_ERROR;
}
for (std::vector<int> ix = grad_grid_cumulant->new_index();
grad_grid_cumulant->index_ok(ix); grad_grid_cumulant->incr(ix)) {
@ -261,31 +252,33 @@ int colvarbias_reweightaMD::write_cumulant_expansion_pmf(
ix, pmf_grid_cumulant->gradient_finite_diff(ix, n), n);
}
}
grad_grid_cumulant->write_multicol(*grad_grid_os);
grad_grid_cumulant->write_multicol(grad_grid_os);
cvm::proxy->close_output_stream(output_grad);
}
return COLVARS_OK;
}
int colvarbias_reweightaMD::write_count(const std::string& p_output_prefix, bool append) {
int colvarbias_reweightaMD::write_count(const std::string& p_output_prefix, bool keep_open) {
const std::string output_name = p_output_prefix + ".count";
cvm::log("Writing the accelerated MD count file \""+output_name+"\".\n");
if (!append) cvm::backup_file(output_name.c_str());
const std::ios::openmode mode = (append ? std::ios::app : std::ios::out);
std::ostream *grid_count_os = cvm::proxy->output_stream(output_name, mode);
std::ostream &grid_count_os = cvm::proxy->output_stream(output_name, "count file");
if (!grid_count_os) {
return cvm::error("Error opening count file "+output_name+
" for writing.\n", COLVARS_FILE_ERROR);
return COLVARS_FILE_ERROR;
}
grid_count->write_multicol(*grid_count_os);
grid_count->write_multicol(grid_count_os);
if (!keep_open) {
cvm::proxy->close_output_stream(output_name);
}
return COLVARS_OK;
}
void colvarbias_reweightaMD::hist_to_pmf(
colvar_grid_scalar* hist, const colvar_grid_scalar* hist_count) const {
colvar_grid_scalar* hist,
const colvar_grid_scalar* hist_count) const
{
colvarproxy *proxy = cvm::main()->proxy;
if (hist->raw_data_num() == 0) return;
const cvm::real kbt = cvm::boltzmann() * cvm::temperature();
const cvm::real kbt = proxy->boltzmann() * proxy->target_temperature();
bool first_min_element = true;
bool first_max_element = true;
cvm::real min_element = 0;
@ -329,12 +322,15 @@ void colvarbias_reweightaMD::hist_to_pmf(
}
}
void colvarbias_reweightaMD::compute_cumulant_expansion_factor(
const colvar_grid_scalar* hist_dV,
const colvar_grid_scalar* hist_dV_square,
const colvar_grid_scalar* hist_count,
colvar_grid_scalar* cumulant_expansion_factor) const {
const cvm::real beta = 1.0 / (cvm::boltzmann() * cvm::temperature());
colvar_grid_scalar* cumulant_expansion_factor) const
{
colvarproxy *proxy = cvm::main()->proxy;
const cvm::real beta = 1.0 / (proxy->boltzmann() * proxy->target_temperature());
size_t i = 0;
for (i = 0; i < hist_dV->raw_data_num(); ++i) {
const cvm::real count = hist_count->value(i);

12
lib/colvars/colvarbias_histogram_reweight_amd.h
View File

@ -51,21 +51,21 @@ public:
/// @brief output the PMF by the exponential average estimator
/// @param[in] p_output_prefix the prefix of the output file
/// @param[in] append append the output to a .hist file if true
/// @param[in] keep_open Allow writing the history of the PMF
virtual int write_exponential_reweighted_pmf(
const std::string& p_output_prefix, bool append = false);
const std::string& p_output_prefix, bool keep_open = false);
/// @brief output the PMF by the cumulant expansion estimator
/// @param[in] p_output_prefix the prefix of the output file
/// @param[in] append append the output to a .hist file if true
/// @param[in] keep_open Allow writing the history of the expansion
virtual int write_cumulant_expansion_pmf(
const std::string& p_output_prefix, bool append = false);
const std::string& p_output_prefix, bool keep_open = false);
/// @brief output the biased sampling
/// @param[in] p_output_prefix the prefix of the output file
/// @param[in] append append the output to a .hist file if true
/// @param[in] keep_open Allow writing the history of the samples
virtual int write_count(
const std::string& p_output_prefix, bool append = false);
const std::string& p_output_prefix, bool keep_open = false);
protected:
/// Current accelMD factor is the from previous frame
std::vector<int> previous_bin;

175
lib/colvars/colvarbias_meta.cpp
View File

@ -36,7 +36,6 @@ colvarbias_meta::colvarbias_meta(char const *key)
: colvarbias(key), colvarbias_ti(key)
{
new_hills_begin = hills.end();
hills_traj_os = NULL;
hill_weight = 0.0;
hill_width = 0.0;
@ -268,28 +267,31 @@ int colvarbias_meta::init_well_tempered_params(std::string const &conf)
int colvarbias_meta::init_ebmeta_params(std::string const &conf)
{
int error_code = COLVARS_OK;
// for ebmeta
target_dist = NULL;
get_keyval(conf, "ebMeta", ebmeta, false);
if(ebmeta){
cvm::main()->cite_feature("Ensemble-biased metadynamics (ebMetaD)");
if (use_grids && expand_grids) {
cvm::error("Error: expandBoundaries is not supported with "
"ebMeta please allocate wide enough boundaries for "
"each colvar ahead of time and set targetdistfile "
"accordingly.\n", COLVARS_INPUT_ERROR);
error_code |= cvm::error("Error: expandBoundaries is not supported with "
"ebMeta; please allocate wide enough boundaries "
"for each colvar ahead of time and set "
"targetDistFile accordingly.\n",
COLVARS_INPUT_ERROR);
}
target_dist = new colvar_grid_scalar();
target_dist->init_from_colvars(colvars);
error_code |= target_dist->init_from_colvars(colvars);
std::string target_dist_file;
get_keyval(conf, "targetDistFile", target_dist_file);
std::ifstream targetdiststream(target_dist_file.c_str());
target_dist->read_multicol(targetdiststream);
error_code |= target_dist->read_multicol(target_dist_file,
"ebMeta target histogram");
cvm::real min_val = target_dist->minimum_value();
cvm::real max_val = target_dist->maximum_value();
if(min_val<0){
cvm::error("Error: Target distribution of EBMetaD "
"has negative values!.\n", COLVARS_INPUT_ERROR);
if (min_val < 0.0) {
error_code |= cvm::error("Error: Target distribution of EBMetaD "
"has negative values!.\n",
COLVARS_INPUT_ERROR);
}
cvm::real target_dist_min_val;
get_keyval(conf, "targetDistMinVal", target_dist_min_val, 1/1000000.0);
@ -301,17 +303,19 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
cvm::log("NOTE: targetDistMinVal is set to zero, the minimum value of the target \n");
cvm::log(" distribution will be set as the minimum positive value.\n");
cvm::real min_pos_val = target_dist->minimum_pos_value();
if(min_pos_val<=0){
cvm::error("Error: Target distribution of EBMetaD has negative "
"or zero minimum positive value!.\n", COLVARS_INPUT_ERROR);
if (min_pos_val <= 0.0){
error_code |= cvm::error("Error: Target distribution of EBMetaD has "
"negative or zero minimum positive value.\n",
COLVARS_INPUT_ERROR);
}
if(min_val==0){
if (min_val == 0.0){
cvm::log("WARNING: Target distribution has zero values.\n");
cvm::log("Zeros will be converted to the minimum positive value.\n");
target_dist->remove_small_values(min_pos_val);
}
} else {
cvm::error("Error: targetDistMinVal must be a value between 0 and 1!.\n", COLVARS_INPUT_ERROR);
error_code |= cvm::error("Error: targetDistMinVal must be a value "
"between 0 and 1.\n", COLVARS_INPUT_ERROR);
}
}
// normalize target distribution and multiply by effective volume = exp(differential entropy)
@ -321,23 +325,18 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, ebmeta_equil_steps);
}
return COLVARS_OK;
return error_code;
}
colvarbias_meta::~colvarbias_meta()
{
colvarbias_meta::clear_state_data();
colvarproxy *proxy = cvm::proxy;
colvarproxy *proxy = cvm::main()->proxy;
if (proxy->get_output_stream(replica_hills_file)) {
proxy->close_output_stream(replica_hills_file);
}
if (hills_traj_os) {
proxy->close_output_stream(hills_traj_file_name());
hills_traj_os = NULL;
}
if (target_dist) {
delete target_dist;
@ -392,9 +391,12 @@ colvarbias_meta::add_hill(colvarbias_meta::hill const &h)
}
// output to trajectory (if specified)
if (hills_traj_os) {
*hills_traj_os << (hills.back()).output_traj();
cvm::proxy->flush_output_stream(hills_traj_os);
if (b_hills_traj) {
// Open trajectory file or access the one already open
std::ostream &hills_traj_os =
cvm::proxy->output_stream(hills_traj_file_name());
hills_traj_os << (hills.back()).output_traj();
cvm::proxy->flush_output_stream(hills_traj_file_name());
}
has_data = true;
@ -424,12 +426,14 @@ colvarbias_meta::delete_hill(hill_iter &h)
}
}
if (hills_traj_os) {
if (b_hills_traj) {
// output to the trajectory
*hills_traj_os << "# DELETED this hill: "
std::ostream &hills_traj_os =
cvm::proxy->output_stream(hills_traj_file_name());
hills_traj_os << "# DELETED this hill: "
<< (hills.back()).output_traj()
<< "\n";
cvm::proxy->flush_output_stream(hills_traj_os);
cvm::proxy->flush_output_stream(hills_traj_file_name());
}
return hills.erase(h);
@ -573,6 +577,7 @@ int colvarbias_meta::update_grid_params()
int colvarbias_meta::update_bias()
{
colvarproxy *proxy = cvm::main()->proxy;
// add a new hill if the required time interval has passed
if (((cvm::step_absolute() % new_hill_freq) == 0) &&
can_accumulate_data() && is_enabled(f_cvb_history_dependent)) {
@ -603,7 +608,7 @@ int colvarbias_meta::update_bias()
} else {
calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here, NULL);
}
hills_scale *= cvm::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
hills_scale *= cvm::exp(-1.0*hills_energy_sum_here/(bias_temperature*proxy->boltzmann()));
}
switch (comm) {
@ -618,10 +623,10 @@ int colvarbias_meta::update_bias()
case multiple_replicas:
add_hill(hill(cvm::step_absolute(), hill_weight*hills_scale,
colvar_values, colvar_sigmas, replica_id));
std::ostream *replica_hills_os =
cvm::proxy->get_output_stream(replica_hills_file);
std::ostream &replica_hills_os =
cvm::proxy->output_stream(replica_hills_file);
if (replica_hills_os) {
*replica_hills_os << hills.back();
replica_hills_os << hills.back();
} else {
return cvm::error("Error: in metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
@ -979,25 +984,24 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first
int colvarbias_meta::replica_share()
{
int error_code = COLVARS_OK;
colvarproxy *proxy = cvm::proxy;
// sync with the other replicas (if needed)
if (comm == multiple_replicas) {
// reread the replicas registry
update_replicas_registry();
error_code |= update_replicas_registry();
// empty the output buffer
std::ostream *replica_hills_os =
proxy->get_output_stream(replica_hills_file);
if (replica_hills_os) {
proxy->flush_output_stream(replica_hills_os);
error_code |= proxy->flush_output_stream(replica_hills_file);
error_code |= read_replica_files();
}
read_replica_files();
}
return COLVARS_OK;
return error_code;
}
void colvarbias_meta::update_replicas_registry()
int colvarbias_meta::update_replicas_registry()
{
int error_code = COLVARS_OK;
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
": updating the list of replicas, currently containing "+
@ -1012,8 +1016,9 @@ void colvarbias_meta::update_replicas_registry()
while (colvarparse::getline_nocomments(reg_file, line))
replicas_registry.append(line+"\n");
} else {
cvm::error("Error: failed to open file \""+replicas_registry_file+
"\" for reading.\n", COLVARS_FILE_ERROR);
error_code |= cvm::error("Error: failed to open file \""+
replicas_registry_file+"\" for reading.\n",
COLVARS_FILE_ERROR);
}
}
@ -1081,7 +1086,7 @@ void colvarbias_meta::update_replicas_registry()
}
}
} else {
cvm::error("Error: cannot read the replicas registry file \""+
error_code |= cvm::error("Error: cannot read the replicas registry file \""+
replicas_registry+"\".\n", COLVARS_FILE_ERROR);
}
@ -1122,10 +1127,12 @@ void colvarbias_meta::update_replicas_registry()
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\": the list of replicas contains "+
cvm::to_str(replicas.size())+" elements.\n");
return error_code;
}
void colvarbias_meta::read_replica_files()
int colvarbias_meta::read_replica_files()
{
// Note: we start from the 2nd replica.
for (size_t ir = 1; ir < replicas.size(); ir++) {
@ -1250,6 +1257,7 @@ void colvarbias_meta::read_replica_files()
" steps. Ensure that it is still running.\n");
}
}
return COLVARS_OK;
}
@ -1413,6 +1421,10 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
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();
if (cvm::debug()) {
cvm::log("Before reading hills from the state file, there are "+
cvm::to_str(hills.size())+" hills in memory.\n");
}
// Read any hills following the grid data (if any)
while (read_hill(is)) {
@ -1431,6 +1443,10 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
if (existing_hills) {
hills.erase(hills.begin(), old_hills_end);
hills_off_grid.erase(hills_off_grid.begin(), old_hills_off_grid_end);
if (cvm::debug()) {
cvm::log("After pruning the old hills, there are now "+
cvm::to_str(hills.size())+" hills in memory.\n");
}
}
if (rebin_grids) {
@ -1614,6 +1630,8 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
int colvarbias_meta::setup_output()
{
int error_code = COLVARS_OK;
output_prefix = cvm::output_prefix();
if (cvm::main()->num_biases_feature(colvardeps::f_cvb_calc_pmf) > 1) {
// if this is not the only free energy integrator, append
@ -1626,8 +1644,11 @@ int colvarbias_meta::setup_output()
// TODO: one may want to specify the path manually for intricated filesystems?
char *pwd = new char[3001];
if (GETCWD(pwd, 3000) == NULL)
cvm::error("Error: cannot get the path of the current working directory.\n");
if (GETCWD(pwd, 3000) == NULL) {
return cvm::error("Error: cannot get the path of the current working directory.\n",
COLVARS_BUG_ERROR);
}
replica_list_file =
(std::string(pwd)+std::string(PATHSEP)+
this->name+"."+replica_id+".files.txt");
@ -1680,38 +1701,35 @@ int colvarbias_meta::setup_output()
// if we're running without grids, use a growing list of "hills" files
// otherwise, just one state file and one "hills" file as buffer
std::ostream *list_os =
cvm::proxy->output_stream(replica_list_file,
(use_grids ? std::ios_base::trunc :
std::ios_base::app));
if (!list_os) {
return cvm::get_error();
}
*list_os << "stateFile " << replica_state_file << "\n";
*list_os << "hillsFile " << replica_hills_file << "\n";
std::ostream &list_os = cvm::proxy->output_stream(replica_list_file);
if (list_os) {
list_os << "stateFile " << replica_state_file << "\n";
list_os << "hillsFile " << replica_hills_file << "\n";
cvm::proxy->close_output_stream(replica_list_file);
} else {
error_code |= COLVARS_FILE_ERROR;
}
// finally, add a new record for this replica to the registry
if (! registered_replica) {
std::ostream *reg_os =
cvm::proxy->output_stream(replicas_registry_file,
std::ios::app);
std::ofstream reg_os(replicas_registry_file.c_str(), std::ios::app);
if (!reg_os) {
return cvm::get_error();
}
*reg_os << replica_id << " " << replica_list_file << "\n";
reg_os << replica_id << " " << replica_list_file << "\n";
cvm::proxy->close_output_stream(replicas_registry_file);
}
}
if (b_hills_traj) {
std::ostream &hills_traj_os =
cvm::proxy->output_stream(hills_traj_file_name());
if (!hills_traj_os) {
hills_traj_os = cvm::proxy->output_stream(hills_traj_file_name());
if (!hills_traj_os) return cvm::get_error();
error_code |= COLVARS_FILE_ERROR;
}
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
return error_code;
}
@ -1804,6 +1822,7 @@ int colvarbias_meta::write_output_files()
void colvarbias_meta::write_pmf()
{
colvarproxy *proxy = cvm::main()->proxy;
// allocate a new grid to store the pmf
colvar_grid_scalar *pmf = new colvar_grid_scalar(*hills_energy);
pmf->setup();
@ -1820,7 +1839,7 @@ void colvarbias_meta::write_pmf()
cvm::real target_val=target_dist->value(i);
if (target_val>0) {
pmf_val=pmf->value(i);
pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * cvm::logn(target_val);
pmf_val=pmf_val + proxy->target_temperature() * proxy->boltzmann() * cvm::logn(target_val);
}
pmf->set_value(i,pmf_val);
}
@ -1830,7 +1849,7 @@ void colvarbias_meta::write_pmf()
pmf->add_constant(-1.0 * max);
pmf->multiply_constant(-1.0);
if (well_tempered) {
cvm::real const well_temper_scale = (bias_temperature + cvm::temperature()) / bias_temperature;
cvm::real const well_temper_scale = (bias_temperature + proxy->target_temperature()) / bias_temperature;
pmf->multiply_constant(well_temper_scale);
}
{
@ -1839,10 +1858,7 @@ void colvarbias_meta::write_pmf()
(dump_fes_save ?
"."+cvm::to_str(cvm::step_absolute()) : "") +
".pmf");
cvm::proxy->backup_file(fes_file_name);
std::ostream *fes_os = cvm::proxy->output_stream(fes_file_name);
pmf->write_multicol(*fes_os);
cvm::proxy->close_output_stream(fes_file_name);
pmf->write_multicol(fes_file_name, "PMF file");
}
}
@ -1861,7 +1877,7 @@ void colvarbias_meta::write_pmf()
cvm::real target_val=target_dist->value(i);
if (target_val>0) {
pmf_val=pmf->value(i);
pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * cvm::logn(target_val);
pmf_val=pmf_val + proxy->target_temperature() * proxy->boltzmann() * cvm::logn(target_val);
}
pmf->set_value(i,pmf_val);
}
@ -1871,17 +1887,14 @@ void colvarbias_meta::write_pmf()
pmf->add_constant(-1.0 * max);
pmf->multiply_constant(-1.0);
if (well_tempered) {
cvm::real const well_temper_scale = (bias_temperature + cvm::temperature()) / bias_temperature;
cvm::real const well_temper_scale = (bias_temperature + proxy->target_temperature()) / bias_temperature;
pmf->multiply_constant(well_temper_scale);
}
std::string const fes_file_name(this->output_prefix +
(dump_fes_save ?
"."+cvm::to_str(cvm::step_absolute()) : "") +
".pmf");
cvm::proxy->backup_file(fes_file_name);
std::ostream *fes_os = cvm::proxy->output_stream(fes_file_name);
pmf->write_multicol(*fes_os);
cvm::proxy->close_output_stream(fes_file_name);
pmf->write_multicol(fes_file_name, "partial PMF file");
}
delete pmf;
@ -1902,9 +1915,9 @@ int colvarbias_meta::write_replica_state_file()
// Write to temporary state file
std::string const tmp_state_file(replica_state_file+".tmp");
error_code |= proxy->remove_file(tmp_state_file);
std::ostream *rep_state_os = cvm::proxy->output_stream(tmp_state_file);
std::ostream &rep_state_os = cvm::proxy->output_stream(tmp_state_file);
if (rep_state_os) {
if (!write_state(*rep_state_os)) {
if (!write_state(rep_state_os)) {
error_code |= cvm::error("Error: in writing to temporary file \""+
tmp_state_file+"\".\n", COLVARS_FILE_ERROR);
}
@ -1921,13 +1934,13 @@ int colvarbias_meta::reopen_replica_buffer_file()
{
int error_code = COLVARS_OK;
colvarproxy *proxy = cvm::proxy;
if (proxy->get_output_stream(replica_hills_file) != NULL) {
if (proxy->output_stream(replica_hills_file)) {
error_code |= proxy->close_output_stream(replica_hills_file);
}
error_code |= proxy->remove_file(replica_hills_file);
std::ostream *replica_hills_os = proxy->output_stream(replica_hills_file);
std::ostream &replica_hills_os = proxy->output_stream(replica_hills_file);
if (replica_hills_os) {
replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
replica_hills_os.setf(std::ios::scientific, std::ios::floatfield);
} else {
error_code |= COLVARS_FILE_ERROR;
}

9
lib/colvars/colvarbias_meta.h
View File

@ -12,8 +12,7 @@
#include <vector>
#include <list>
#include <sstream>
#include <fstream>
#include <iosfwd>
#include "colvarbias.h"
#include "colvargrid.h"
@ -85,8 +84,6 @@ protected:
/// Write the hill logfile
bool b_hills_traj;
/// Logfile of hill management (creation and deletion)
std::ostream *hills_traj_os;
/// Name of the hill logfile
std::string const hills_traj_file_name() const;
@ -214,10 +211,10 @@ protected:
std::string replica_file_name;
/// \brief Read the existing replicas on registry
virtual void update_replicas_registry();
virtual int update_replicas_registry();
/// \brief Read new data from replicas' files
virtual void read_replica_files();
virtual int read_replica_files();
/// Write full state information to be read by other replicas
virtual int write_replica_state_file();

137
lib/colvars/colvarbias_restraint.cpp
View File

@ -7,6 +7,10 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <fstream>
#include <iostream>
#include <iomanip>
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "colvarvalue.h"
@ -196,6 +200,8 @@ int colvarbias_restraint_moving::init(std::string const &conf)
if (b_chg_centers || b_chg_force_k) {
first_step = cvm::step_absolute();
get_keyval(conf, "targetNumSteps", target_nsteps, target_nsteps);
if (!target_nsteps) {
cvm::error("Error: targetNumSteps must be non-zero.\n", COLVARS_INPUT_ERROR);
@ -335,13 +341,17 @@ int colvarbias_restraint_centers_moving::update_centers(cvm::real lambda)
int colvarbias_restraint_centers_moving::update()
{
if (!cvm::main()->proxy->simulation_running()) {
return COLVARS_OK;
}
if (b_chg_centers) {
if (target_nstages) {
// Staged update
if (stage <= target_nstages) {
if ((cvm::step_relative() > 0) &&
((cvm::step_absolute() % target_nsteps) == 1)) {
(((cvm::step_absolute() - first_step) % target_nsteps) == 1)) {
cvm::real const lambda =
cvm::real(stage)/cvm::real(target_nstages);
update_centers(lambda);
@ -358,9 +368,9 @@ int colvarbias_restraint_centers_moving::update()
}
} else {
// Continuous update
if (cvm::step_absolute() <= target_nsteps) {
if (cvm::step_absolute() - first_step <= target_nsteps) {
cvm::real const lambda =
cvm::real(cvm::step_absolute())/cvm::real(target_nsteps);
cvm::real(cvm::step_absolute() - first_step)/cvm::real(target_nsteps);
update_centers(lambda);
} else {
for (size_t i = 0; i < num_variables(); i++) {
@ -389,10 +399,13 @@ int colvarbias_restraint_centers_moving::update()
int colvarbias_restraint_centers_moving::update_acc_work()
{
if (!cvm::main()->proxy->simulation_running()) {
return COLVARS_OK;
}
if (b_chg_centers) {
if (is_enabled(f_cvb_output_acc_work)) {
if ((cvm::step_relative() > 0) &&
(cvm::step_absolute() <= target_nsteps)) {
(cvm::step_absolute() - first_step <= target_nsteps)) {
for (size_t i = 0; i < num_variables(); i++) {
// project forces on the calculated increments at this step
acc_work += colvar_forces[i] * centers_incr[i];
@ -496,10 +509,11 @@ colvarbias_restraint_k_moving::colvarbias_restraint_k_moving(char const *key)
colvarbias_restraint_moving(key)
{
b_chg_force_k = false;
b_decoupling = false;
target_equil_steps = 0;
target_force_k = -1.0;
starting_force_k = -1.0;
force_k_exp = 1.0;
lambda_exp = 1.0;
restraint_FE = 0.0;
force_k_incr = 0.0;
}
@ -509,18 +523,29 @@ int colvarbias_restraint_k_moving::init(std::string const &conf)
{
colvarbias_restraint_k::init(conf);
get_keyval(conf, "decoupling", b_decoupling, b_decoupling);
if (b_decoupling) {
starting_force_k = 0.0;
target_force_k = force_k;
b_chg_force_k = true;
}
if (get_keyval(conf, "targetForceConstant", target_force_k, target_force_k)) {
if (b_decoupling) {
cvm::error("Error: targetForceConstant may not be specified together with decoupling.\n", COLVARS_INPUT_ERROR);
return COLVARS_ERROR;
}
starting_force_k = force_k;
b_chg_force_k = true;
}
if (b_chg_force_k) {
// parse moving restraint options
colvarbias_restraint_moving::init(conf);
} else {
if (!b_chg_force_k) {
return COLVARS_OK;
}
// parse moving restraint options
colvarbias_restraint_moving::init(conf);
get_keyval(conf, "targetEquilSteps", target_equil_steps, target_equil_steps);
if (get_keyval(conf, "lambdaSchedule", lambda_schedule, lambda_schedule) &&
@ -534,12 +559,13 @@ int colvarbias_restraint_k_moving::init(std::string const &conf)
target_nstages = lambda_schedule.size() - 1;
}
if (get_keyval(conf, "targetForceExponent", force_k_exp, force_k_exp)) {
if (! b_chg_force_k)
cvm::log("Warning: not changing force constant: targetForceExponent will be ignored\n");
if ((get_keyval(conf, "targetForceExponent", lambda_exp, lambda_exp, parse_deprecated)
|| get_keyval(conf, "lambdaExponent", lambda_exp, lambda_exp))
&& !b_chg_force_k) {
cvm::error("Error: cannot set lambdaExponent unless a changing force constant is active.\n", COLVARS_INPUT_ERROR);
}
if (force_k_exp < 1.0) {
cvm::log("Warning: for all practical purposes, targetForceExponent should be 1.0 or greater.\n");
if (lambda_exp < 1.0) {
cvm::log("Warning: for all practical purposes, lambdaExponent should be 1.0 or greater.\n");
}
return COLVARS_OK;
@ -548,24 +574,27 @@ int colvarbias_restraint_k_moving::init(std::string const &conf)
int colvarbias_restraint_k_moving::update()
{
if (!cvm::main()->proxy->simulation_running()) {
return COLVARS_OK;
}
if (b_chg_force_k) {
cvm::real lambda;
if (target_nstages) {
if (cvm::step_absolute() == 0) {
if (cvm::step_absolute() == first_step) {
// Setup first stage of staged variable force constant calculation
if (lambda_schedule.size()) {
lambda = lambda_schedule[0];
} else {
lambda = 0.0;
lambda = (b_decoupling ? 1.0 : 0.0);
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* cvm::pow(lambda, force_k_exp);
* cvm::pow(lambda, lambda_exp);
cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage)
+ " : lambda = " + cvm::to_str(lambda)
+ ", k = " + cvm::to_str(force_k));
+ ", k = " + cvm::to_str(force_k)+"\n");
}
// TI calculation: estimate free energy derivative
@ -574,9 +603,10 @@ int colvarbias_restraint_k_moving::update()
lambda = lambda_schedule[stage];
} else {
lambda = cvm::real(stage) / cvm::real(target_nstages);
if (b_decoupling) lambda = 1.0 - lambda;
}
if (target_equil_steps == 0 || cvm::step_absolute() % target_nsteps >= target_equil_steps) {
if (target_equil_steps == 0 || (cvm::step_absolute() - first_step) % target_nsteps >= target_equil_steps) {
// Start averaging after equilibration period, if requested
// Derivative of energy with respect to force_k
@ -584,17 +614,17 @@ int colvarbias_restraint_k_moving::update()
for (size_t i = 0; i < num_variables(); i++) {
dU_dk += d_restraint_potential_dk(i);
}
restraint_FE += force_k_exp * cvm::pow(lambda, force_k_exp - 1.0)
restraint_FE += lambda_exp * cvm::pow(lambda, lambda_exp - 1.0)
* (target_force_k - starting_force_k) * dU_dk;
}
// Finish current stage...
if (cvm::step_absolute() % target_nsteps == 0 &&
cvm::step_absolute() > 0) {
if ((cvm::step_absolute() - first_step) % target_nsteps == 0 &&
cvm::step_absolute() > first_step) {
cvm::log("Restraint " + this->name + " Lambda= "
+ cvm::to_str(lambda) + " dA/dLambda= "
+ cvm::to_str(restraint_FE / cvm::real(target_nsteps - target_equil_steps)));
+ cvm::to_str(restraint_FE / cvm::real(target_nsteps - target_equil_steps))+"\n");
// ...and move on to the next one
if (stage < target_nstages) {
@ -605,23 +635,24 @@ int colvarbias_restraint_k_moving::update()
lambda = lambda_schedule[stage];
} else {
lambda = cvm::real(stage) / cvm::real(target_nstages);
if (b_decoupling) lambda = 1.0 - lambda;
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* cvm::pow(lambda, force_k_exp);
* cvm::pow(lambda, lambda_exp);
cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage)
+ " : lambda = " + cvm::to_str(lambda)
+ ", k = " + cvm::to_str(force_k));
+ ", k = " + cvm::to_str(force_k)+"\n");
}
}
} else if (cvm::step_absolute() <= target_nsteps) {
} else if (cvm::step_absolute() - first_step <= target_nsteps) {
// update force constant (slow growth)
lambda = cvm::real(cvm::step_absolute()) / cvm::real(target_nsteps);
lambda = cvm::real(cvm::step_absolute() - first_step) / cvm::real(target_nsteps);
if (b_decoupling) lambda = 1.0 - lambda;
cvm::real const force_k_old = force_k;
force_k = starting_force_k + (target_force_k - starting_force_k)
* cvm::pow(lambda, force_k_exp);
* cvm::pow(lambda, lambda_exp);
force_k_incr = force_k - force_k_old;
}
}
@ -632,6 +663,9 @@ int colvarbias_restraint_k_moving::update()
int colvarbias_restraint_k_moving::update_acc_work()
{
if (!cvm::main()->proxy->simulation_running()) {
return COLVARS_OK;
}
if (b_chg_force_k) {
if (is_enabled(f_cvb_output_acc_work)) {
if (cvm::step_relative() > 0) {
@ -980,7 +1014,7 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
}
// Initialize starting value of the force constant (in case it's changing)
starting_force_k = force_k;
starting_force_k = (b_decoupling ? 0.0 : force_k);
if (lower_walls.size() > 0) {
for (i = 0; i < num_variables(); i++) {
@ -1302,6 +1336,8 @@ colvarbias_restraint_histogram::colvarbias_restraint_histogram(char const *key)
int colvarbias_restraint_histogram::init(std::string const &conf)
{
int error_code = COLVARS_OK;
colvarbias::init(conf);
enable(f_cvb_apply_force);
@ -1312,14 +1348,15 @@ int colvarbias_restraint_histogram::init(std::string const &conf)
get_keyval(conf, "width", width, width);
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", COLVARS_INPUT_ERROR);
error_code |= cvm::error("Error: \"width\" must be positive.\n",
COLVARS_INPUT_ERROR);
}
get_keyval(conf, "gaussianWidth", gaussian_width, 2.0 * width, colvarparse::parse_silent);
get_keyval(conf, "gaussianSigma", gaussian_width, 2.0 * width);
if (lower_boundary >= upper_boundary) {
cvm::error("Error: the upper boundary, "+
error_code |= cvm::error("Error: the upper boundary, "+
cvm::to_str(upper_boundary)+
", is not higher than the lower boundary, "+
cvm::to_str(lower_boundary)+".\n",
@ -1347,22 +1384,30 @@ int colvarbias_restraint_histogram::init(std::string const &conf)
get_keyval(conf, "refHistogramFile", ref_p_file, std::string(""));
if (ref_p_file.size()) {
if (inline_ref_p) {
cvm::error("Error: cannot specify both refHistogram and refHistogramFile at the same time.\n",
error_code |= cvm::error("Error: cannot specify both refHistogram and refHistogramFile at the same time.\n",
COLVARS_INPUT_ERROR);
} else {
std::ifstream is(ref_p_file.c_str());
std::istream &is =
cvm::main()->proxy->input_stream(ref_p_file,
"reference histogram file");
std::string data_s = "";
std::string line;
while (getline_nocomments(is, line)) {
data_s.append(line+"\n");
}
if (data_s.size() == 0) {
cvm::error("Error: file \""+ref_p_file+"\" empty or unreadable.\n", COLVARS_FILE_ERROR);
error_code |= cvm::error("Error: file \""+ref_p_file+
"\" empty or unreadable.\n",
COLVARS_FILE_ERROR);
}
is.close();
error_code |= cvm::main()->proxy->close_input_stream(ref_p_file);
cvm::vector1d<cvm::real> data;
if (data.from_simple_string(data_s) != 0) {
cvm::error("Error: could not read histogram from file \""+ref_p_file+"\".\n");
error_code |= cvm::error("Error: could not read histogram from file \""+
ref_p_file+"\".\n");
}
if (data.size() == 2*ref_p.size()) {
// file contains both x and p(x)
@ -1373,11 +1418,13 @@ int colvarbias_restraint_histogram::init(std::string const &conf)
} else if (data.size() == ref_p.size()) {
ref_p = data;
} else {
cvm::error("Error: file \""+ref_p_file+"\" contains a histogram of different length.\n",
error_code |= cvm::error("Error: file \""+ref_p_file+
"\" contains a histogram of different length.\n",
COLVARS_INPUT_ERROR);
}
}
}
cvm::real const ref_integral = ref_p.sum() * width;
if (cvm::fabs(ref_integral - 1.0) > 1.0e-03) {
cvm::log("Reference distribution not normalized, normalizing to unity.\n");
@ -1387,7 +1434,7 @@ int colvarbias_restraint_histogram::init(std::string const &conf)
get_keyval(conf, "writeHistogram", b_write_histogram, false);
get_keyval(conf, "forceConstant", force_k, 1.0);
return COLVARS_OK;
return error_code;
}
@ -1492,18 +1539,20 @@ int colvarbias_restraint_histogram::update()
int colvarbias_restraint_histogram::write_output_files()
{
if (b_write_histogram) {
colvarproxy *proxy = cvm::main()->proxy;
std::string file_name(cvm::output_prefix()+"."+this->name+".hist.dat");
std::ostream *os = cvm::proxy->output_stream(file_name);
*os << "# " << cvm::wrap_string(variables(0)->name, cvm::cv_width)
std::ostream &os = proxy->output_stream(file_name,
"histogram output file");
os << "# " << cvm::wrap_string(variables(0)->name, cvm::cv_width)
<< " " << "p(" << cvm::wrap_string(variables(0)->name, cvm::cv_width-3)
<< ")\n";
os->setf(std::ios::fixed, std::ios::floatfield);
os.setf(std::ios::fixed, std::ios::floatfield);
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+1)*width);
*os << " "
os << " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< x_grid
@ -1512,7 +1561,7 @@ int colvarbias_restraint_histogram::write_output_files()
<< std::setw(cvm::cv_width)
<< p[igrid] << "\n";
}
cvm::proxy->close_output_stream(file_name);
proxy->close_output_stream(file_name);
}
return COLVARS_OK;
}

8
lib/colvars/colvarbias_restraint.h
View File

@ -123,6 +123,9 @@ protected:
/// \brief Changing force constant?
bool b_chg_force_k;
/// \brief Perform decoupling of the restraint?
bool b_decoupling;
/// \brief Number of stages over which to perform the change
/// If zero, perform a continuous change
int target_nstages;
@ -137,6 +140,9 @@ protected:
/// or restraint centers
cvm::step_number target_nsteps;
/// \brief Timestep at which the restraint starts moving
cvm::step_number first_step;
/// \brief Accumulated work (computed when outputAccumulatedWork == true)
cvm::real acc_work;
};
@ -207,7 +213,7 @@ protected:
cvm::real starting_force_k;
/// \brief Exponent for varying the force constant
cvm::real force_k_exp;
cvm::real lambda_exp;
/// \brief Intermediate quantity to compute the restraint free energy
/// (in TI, would be the accumulating FE derivative)

2
lib/colvars/colvarcomp.h
View File

@ -616,7 +616,7 @@ public:
dipole_magnitude (std::string const &conf);
dipole_magnitude (cvm::atom const &a1);
dipole_magnitude();
virtual inline ~dipole_magnitude() {}
virtual ~dipole_magnitude() {}
virtual void calc_value();
virtual void calc_gradients();
//virtual void calc_force_invgrads();

45
lib/colvars/colvarcomp_combination.cpp
View File

@ -141,13 +141,15 @@ void colvar::linearCombination::apply_force(colvarvalue const &force) {
colvar::customColvar::customColvar(std::string const &conf): linearCombination(conf) {
use_custom_function = false;
// code swipe from colvar::init_custom_function
#ifdef LEPTON
std::string expr_in, expr;
size_t pos = 0; // current position in config string
#ifdef LEPTON
std::vector<Lepton::ParsedExpression> pexprs;
Lepton::ParsedExpression pexpr;
double *ref;
size_t pos = 0; // current position in config string
#endif
if (key_lookup(conf, "customFunction", &expr_in, &pos)) {
#ifdef LEPTON
use_custom_function = true;
cvm::log("This colvar uses a custom function.\n");
do {
@ -208,11 +210,15 @@ colvar::customColvar::customColvar(std::string const &conf): linearCombination(c
} else {
x.type(colvarvalue::type_scalar);
}
} else {
cvm::log(std::string{"Warning: no customFunction specified.\n"});
cvm::log(std::string{"Warning: use linear combination instead.\n"});
}
#else
cvm::error("customFunction requires the Lepton library, but it is not enabled during compilation.\n"
"Please refer to the Compilation Notes section of the Colvars manual for more information.\n",
COLVARS_INPUT_ERROR);
#endif
} else {
cvm::log("Warning: no customFunction specified.\n");
cvm::log("Warning: use linear combination instead.\n");
}
}
colvar::customColvar::~customColvar() {
@ -227,6 +233,9 @@ colvar::customColvar::~customColvar() {
}
void colvar::customColvar::calc_value() {
if (!use_custom_function) {
colvar::linearCombination::calc_value();
} else {
#ifdef LEPTON
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
cv[i_cv]->calc_value();
@ -246,13 +255,18 @@ void colvar::customColvar::calc_value() {
}
x[i] = value_evaluators[i]->evaluate();
}
#else
cvm::error("customFunction requires the Lepton library, but it is not enabled during compilation.\n"
"Please refer to the Compilation Notes section of the Colvars manual for more information.\n",
COLVARS_INPUT_ERROR);
#endif
if (!use_custom_function) {
colvar::linearCombination::calc_value();
}
}
void colvar::customColvar::calc_gradients() {
if (!use_custom_function) {
colvar::linearCombination::calc_gradients();
} else {
#ifdef LEPTON
size_t r = 0; // index in the vector of variable references
size_t e = 0; // index of the gradient evaluator
@ -279,13 +293,18 @@ void colvar::customColvar::calc_gradients() {
}
}
}
#else
cvm::error("customFunction requires the Lepton library, but it is not enabled during compilation.\n"
"Please refer to the Compilation Notes section of the Colvars manual for more information.\n",
COLVARS_INPUT_ERROR);
#endif
if (!use_custom_function) {
colvar::linearCombination::calc_gradients();
}
}
void colvar::customColvar::apply_force(colvarvalue const &force) {
if (!use_custom_function) {
colvar::linearCombination::apply_force(force);
} else {
#ifdef LEPTON
size_t r = 0; // index in the vector of variable references
size_t e = 0; // index of the gradient evaluator
@ -314,9 +333,11 @@ void colvar::customColvar::apply_force(colvarvalue const &force) {
cv[i_cv]->apply_force(cv_force);
}
}
#else
cvm::error("customFunction requires the Lepton library, but it is not enabled during compilation.\n"
"Please refer to the Compilation Notes section of the Colvars manual for more information.\n",
COLVARS_INPUT_ERROR);
#endif
if (!use_custom_function) {
colvar::linearCombination::apply_force(force);
}
}

14
lib/colvars/colvarcomp_coordnums.cpp
View File

@ -121,12 +121,12 @@ colvar::coordnum::coordnum(std::string const &conf)
}
bool const b_isotropic = get_keyval(conf, "cutoff", r0,
cvm::real(4.0 * proxy->angstrom_value));
cvm::real(proxy->angstrom_to_internal(4.0)));
if (get_keyval(conf, "cutoff3", r0_vec,
cvm::rvector(4.0 * proxy->angstrom_value,
4.0 * proxy->angstrom_value,
4.0 * proxy->angstrom_value))) {
cvm::rvector(proxy->angstrom_to_internal(4.0),
proxy->angstrom_to_internal(4.0),
proxy->angstrom_to_internal(4.0)))) {
if (b_isotropic) {
cvm::error("Error: cannot specify \"cutoff\" and \"cutoff3\" "
"at the same time.\n",
@ -328,7 +328,7 @@ colvar::h_bond::h_bond(std::string const &conf)
atom_groups[0]->add_atom(acceptor);
atom_groups[0]->add_atom(donor);
get_keyval(conf, "cutoff", r0, (3.3 * proxy->angstrom_value));
get_keyval(conf, "cutoff", r0, proxy->angstrom_to_internal(3.3));
get_keyval(conf, "expNumer", en, 6);
get_keyval(conf, "expDenom", ed, 8);
@ -405,7 +405,7 @@ colvar::selfcoordnum::selfcoordnum(std::string const &conf)
group1 = parse_group(conf, "group1");
get_keyval(conf, "cutoff", r0, cvm::real(4.0 * proxy->angstrom_value));
get_keyval(conf, "cutoff", r0, cvm::real(proxy->angstrom_to_internal(4.0)));
get_keyval(conf, "expNumer", en, 6);
get_keyval(conf, "expDenom", ed, 12);
@ -556,7 +556,7 @@ colvar::groupcoordnum::groupcoordnum(std::string const &conf)
}
bool const b_scale = get_keyval(conf, "cutoff", r0,
cvm::real(4.0 * proxy->angstrom_value));
cvm::real(proxy->angstrom_to_internal(4.0)));
if (get_keyval(conf, "cutoff3", r0_vec,
cvm::rvector(4.0, 4.0, 4.0), parse_silent)) {

1
lib/colvars/colvarcomp_distances.cpp
View File

@ -1055,6 +1055,7 @@ colvar::rmsd::rmsd(std::string const &conf)
n_permutations = 1;
while (key_lookup(conf, "atomPermutation", &perm_conf, &pos)) {
cvm::main()->cite_feature("Symmetry-adapted RMSD");
std::vector<size_t> perm;
if (perm_conf.size()) {
std::istringstream is(perm_conf);

7
lib/colvars/colvarcomp_gpath.cpp
View File

@ -12,6 +12,7 @@
#include <cmath>
#include <cstdlib>
#include <limits>
#include <fstream>
#include "colvarmodule.h"
#include "colvarvalue.h"
@ -426,9 +427,8 @@ colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
std::string path_filename;
get_keyval(conf, "pathFile", path_filename);
cvm::log(std::string("Reading path file: ") + path_filename + std::string("\n"));
std::ifstream ifs_path(path_filename);
if (!ifs_path.is_open()) {
cvm::error("Error: failed to open path file.\n");
auto &ifs_path = cvm::main()->proxy->input_stream(path_filename);
if (!ifs_path) {
return;
}
std::string line;
@ -459,6 +459,7 @@ colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
++total_reference_frames;
}
}
cvm::main()->proxy->close_input_stream(path_filename);
if (total_reference_frames <= 1) {
cvm::error("Error: there is only 1 or 0 reference frame, which doesn't constitute a path.\n");
return;

13
lib/colvars/colvarcomp_protein.cpp
View File

@ -86,7 +86,7 @@ colvar::alpha_angles::alpha_angles(std::string const &conf)
{
cvm::real r0;
size_t en, ed;
get_keyval(conf, "hBondCutoff", r0, (3.3 * proxy->angstrom_value));
get_keyval(conf, "hBondCutoff", r0, proxy->angstrom_to_internal(3.3));
get_keyval(conf, "hBondExpNumer", en, 6);
get_keyval(conf, "hBondExpDenom", ed, 8);
@ -333,10 +333,11 @@ colvar::dihedPC::dihedPC(std::string const &conf)
return;
}
std::ifstream vecFile;
vecFile.open(vecFileName.c_str());
if (!vecFile.good()) {
cvm::error("Error opening dihedral PCA vector file " + vecFileName + " for reading");
std::istream &vecFile =
cvm::main()->proxy->input_stream(vecFileName,
"dihedral PCA vector file");
if (!vecFile) {
return;
}
// TODO: adapt to different formats by setting this flag
@ -375,7 +376,7 @@ colvar::dihedPC::dihedPC(std::string const &conf)
}
}
*/
vecFile.close();
cvm::main()->proxy->close_input_stream(vecFileName);
} else {
get_keyval(conf, "vector", coeffs, coeffs);

8
lib/colvars/colvarcomp_rotations.cpp
View File

@ -67,15 +67,17 @@ int colvar::orientation::init(std::string const &conf)
}
cvm::log("Centering the reference coordinates: it is "
"assumed that each atom is the closest "
"periodic image to the center of geometry.\n");
cvm::rvector ref_cog(0.0, 0.0, 0.0);
size_t i;
for (i = 0; i < ref_pos.size(); i++) {
ref_cog += ref_pos[i];
}
ref_cog /= cvm::real(ref_pos.size());
cvm::log("Centering the reference coordinates on the origin by subtracting "
"the center of geometry at "+
cvm::to_str(-1.0 * ref_cog)+"; it is "
"assumed that each atom is the closest "
"periodic image to the center of geometry.\n");
for (i = 0; i < ref_pos.size(); i++) {
ref_pos[i] -= ref_cog;
}

121
lib/colvars/colvargrid.cpp
View File

@ -7,14 +7,18 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <ctime>
#include <fstream>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
#include "colvargrid.h"
#include "colvargrid_def.h"
#include <ctime>
colvar_grid_count::colvar_grid_count()
: colvar_grid<size_t>()
@ -33,6 +37,42 @@ colvar_grid_count::colvar_grid_count(std::vector<colvar *> &colvars,
: colvar_grid<size_t>(colvars, def_count, 1, margin)
{}
std::istream & colvar_grid_count::read_multicol(std::istream &is, bool add)
{
return colvar_grid<size_t>::read_multicol(is, add);
}
int colvar_grid_count::read_multicol(std::string const &filename,
std::string description,
bool add)
{
return colvar_grid<size_t>::read_multicol(filename, description, add);
}
std::ostream & colvar_grid_count::write_multicol(std::ostream &os) const
{
return colvar_grid<size_t>::write_multicol(os);
}
int colvar_grid_count::write_multicol(std::string const &filename,
std::string description) const
{
return colvar_grid<size_t>::write_multicol(filename, description);
}
std::ostream & colvar_grid_count::write_opendx(std::ostream &os) const
{
return colvar_grid<size_t>::write_opendx(os);
}
int colvar_grid_count::write_opendx(std::string const &filename,
std::string description) const
{
return colvar_grid<size_t>::write_opendx(filename, description);
}
colvar_grid_scalar::colvar_grid_scalar()
: colvar_grid<cvm::real>(), samples(NULL)
{}
@ -56,6 +96,41 @@ colvar_grid_scalar::~colvar_grid_scalar()
{
}
std::istream & colvar_grid_scalar::read_multicol(std::istream &is, bool add)
{
return colvar_grid<cvm::real>::read_multicol(is, add);
}
int colvar_grid_scalar::read_multicol(std::string const &filename,
std::string description,
bool add)
{
return colvar_grid<cvm::real>::read_multicol(filename, description, add);
}
std::ostream & colvar_grid_scalar::write_multicol(std::ostream &os) const
{
return colvar_grid<cvm::real>::write_multicol(os);
}
int colvar_grid_scalar::write_multicol(std::string const &filename,
std::string description) const
{
return colvar_grid<cvm::real>::write_multicol(filename, description);
}
std::ostream & colvar_grid_scalar::write_opendx(std::ostream &os) const
{
return colvar_grid<cvm::real>::write_opendx(os);
}
int colvar_grid_scalar::write_opendx(std::string const &filename,
std::string description) const
{
return colvar_grid<cvm::real>::write_opendx(filename, description);
}
cvm::real colvar_grid_scalar::maximum_value() const
{
cvm::real max = data[0];
@ -145,10 +220,9 @@ colvar_grid_gradient::colvar_grid_gradient(std::string &filename)
samples(NULL),
weights(NULL)
{
std::ifstream is;
is.open(filename.c_str());
if (!is.is_open()) {
cvm::error("Error opening multicol gradient file " + filename + " for reading.\n");
std::istream &is = cvm::main()->proxy->input_stream(filename,
"gradient file");
if (!is) {
return;
}
@ -203,7 +277,42 @@ colvar_grid_gradient::colvar_grid_gradient(std::string &filename)
is.clear();
is.seekg(0);
read_multicol(is);
is.close();
cvm::main()->proxy->close_input_stream(filename);
}
std::istream & colvar_grid_gradient::read_multicol(std::istream &is, bool add)
{
return colvar_grid<cvm::real>::read_multicol(is, add);
}
int colvar_grid_gradient::read_multicol(std::string const &filename,
std::string description,
bool add)
{
return colvar_grid<cvm::real>::read_multicol(filename, description, add);
}
std::ostream & colvar_grid_gradient::write_multicol(std::ostream &os) const
{
return colvar_grid<cvm::real>::write_multicol(os);
}
int colvar_grid_gradient::write_multicol(std::string const &filename,
std::string description) const
{
return colvar_grid<cvm::real>::write_multicol(filename, description);
}
std::ostream & colvar_grid_gradient::write_opendx(std::ostream &os) const
{
return colvar_grid<cvm::real>::write_opendx(os);
}
int colvar_grid_gradient::write_opendx(std::string const &filename,
std::string description) const
{
return colvar_grid<cvm::real>::write_opendx(filename, description);
}

285
lib/colvars/colvargrid.h
View File

@ -732,7 +732,7 @@ public:
/// \brief Return the value suitable for output purposes (so that it
/// may be rescaled or manipulated without changing it permanently)
virtual inline T value_output(std::vector<int> const &ix,
virtual T value_output(std::vector<int> const &ix,
size_t const &imult = 0) const
{
return value(ix, imult);
@ -741,7 +741,7 @@ public:
/// \brief Get the value from a formatted output and transform it
/// into the internal representation (the two may be different,
/// e.g. when using colvar_grid_count)
virtual inline void value_input(std::vector<int> const &ix,
virtual void value_input(std::vector<int> const &ix,
T const &t,
size_t const &imult = 0,
bool add = false)
@ -803,7 +803,7 @@ public:
}
}
/// \brief Write the grid parameters (number of colvars, boundaries, width and number of points)
/// Write the grid parameters (number of colvars, boundaries, width and number of points)
std::ostream & write_params(std::ostream &os)
{
size_t i;
@ -1028,188 +1028,27 @@ public:
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) const
{
std::streamsize const w = os.width();
std::streamsize const p = os.precision();
/// Read a grid written by write_multicol(), incrementing if add is true
std::istream & read_multicol(std::istream &is, bool add = false);
// Data in the header: nColvars, then for each
// xiMin, dXi, nPoints, periodic
/// Read a grid written by write_multicol(), incrementing if add is true
int read_multicol(std::string const &filename,
std::string description = "grid file",
bool add = false);
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";
}
/// Write grid in a format which is both human-readable and gnuplot-friendly
std::ostream & write_multicol(std::ostream &os) const;
/// Write grid in a format which is both human-readable and gnuplot-friendly
int write_multicol(std::string const &filename,
std::string description = "grid file") const;
for (std::vector<int> ix = new_index(); index_ok(ix); incr(ix) ) {
/// Write the grid data without labels, as they are represented in memory
std::ostream & write_opendx(std::ostream &os) const;
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 flag
std::string hash;
cvm::real lower, width, x;
size_t n, periodic_flag;
bool remap;
std::vector<T> new_value;
std::vector<int> nx_read;
std::vector<int> bin;
if ( cv.size() > 0 && cv.size() != nd ) {
cvm::error("Cannot read grid file: number of variables in file differs from number referenced by grid.\n");
return is;
}
if ( !(is >> hash) || (hash != "#") ) {
cvm::error("Error reading grid at position "+
cvm::to_str(static_cast<size_t>(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(static_cast<size_t>(is.tellg()))+
" in stream(read \"" + hash + "\")\n");
return is;
}
is >> lower >> width >> nx_read[i] >> periodic_flag;
if ( (cvm::fabs(lower - lower_boundaries[i].real_value) > 1.0e-10) ||
(cvm::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;
}
/// \brief Write the grid data without labels, as they are
/// represented in memory
std::ostream & write_opendx(std::ostream &os) const
{
// write the header
os << "object 1 class gridpositions counts";
size_t icv;
for (icv = 0; icv < num_variables(); icv++) {
os << " " << number_of_points(icv);
}
os << "\n";
os << "origin";
for (icv = 0; icv < num_variables(); icv++) {
os << " " << (lower_boundaries[icv].real_value + 0.5 * widths[icv]);
}
os << "\n";
for (icv = 0; icv < num_variables(); icv++) {
os << "delta";
for (size_t icv2 = 0; icv2 < num_variables(); icv2++) {
if (icv == icv2) os << " " << widths[icv];
else os << " " << 0.0;
}
os << "\n";
}
os << "object 2 class gridconnections counts";
for (icv = 0; icv < num_variables(); icv++) {
os << " " << number_of_points(icv);
}
os << "\n";
os << "object 3 class array type double rank 0 items "
<< number_of_points() << " data follows\n";
write_raw(os);
os << "object \"collective variables scalar field\" class field\n";
return os;
}
/// Write the grid data without labels, as they are represented in memory
int write_opendx(std::string const &filename,
std::string description = "grid file") const;
};
@ -1224,7 +1063,7 @@ public:
colvar_grid_count();
/// Destructor
virtual inline ~colvar_grid_count()
virtual ~colvar_grid_count()
{}
/// Constructor
@ -1249,10 +1088,30 @@ public:
return new_data[address(ix) + imult];
}
/// \brief Get the value from a formatted output and transform it
/// into the internal representation (it may have been rescaled or
/// manipulated)
virtual inline void value_input(std::vector<int> const &ix,
/// Read a grid written by write_multicol(), incrementin if data is true
std::istream & read_multicol(std::istream &is, bool add = false);
/// Read a grid written by write_multicol(), incrementin if data is true
int read_multicol(std::string const &filename,
std::string description = "grid file",
bool add = false);
/// Write grid in a format which is both human-readable and gnuplot-friendly
std::ostream & write_multicol(std::ostream &os) const;
/// Write grid in a format which is both human-readable and gnuplot-friendly
int write_multicol(std::string const &filename,
std::string description = "grid file") const;
/// Write the grid data without labels, as they are represented in memory
std::ostream & write_opendx(std::ostream &os) const;
/// Write the grid data without labels, as they are represented in memory
int write_opendx(std::string const &filename,
std::string description = "grid file") const;
/// Enter or add a value, but also handle parent grid
virtual void value_input(std::vector<int> const &ix,
size_t const &t,
size_t const &imult = 0,
bool add = false)
@ -1380,7 +1239,7 @@ public:
colvar_grid_scalar(colvar_grid_scalar const &g);
/// Destructor
~colvar_grid_scalar();
virtual ~colvar_grid_scalar();
/// Constructor from specific sizes arrays
colvar_grid_scalar(std::vector<int> const &nx_i);
@ -1402,6 +1261,28 @@ public:
has_data = true;
}
/// Read a grid written by write_multicol(), incrementin if data is true
std::istream & read_multicol(std::istream &is, bool add = false);
/// Read a grid written by write_multicol(), incrementin if data is true
int read_multicol(std::string const &filename,
std::string description = "grid file",
bool add = false);
/// Write grid in a format which is both human-readable and gnuplot-friendly
std::ostream & write_multicol(std::ostream &os) const;
/// Write grid in a format which is both human-readable and gnuplot-friendly
int write_multicol(std::string const &filename,
std::string description = "grid file") const;
/// Write the grid data without labels, as they are represented in memory
std::ostream & write_opendx(std::ostream &os) const;
/// Write the grid data without labels, as they are represented in memory
int write_opendx(std::string const &filename,
std::string description = "grid file") const;
/// \brief Return the gradient of the scalar field from finite differences
/// Input coordinates are those of gradient grid, shifted wrt scalar grid
/// Should not be called on edges of scalar grid, provided the latter has margins
@ -1517,9 +1398,7 @@ public:
}
}
/// \brief Get the value from a formatted output and transform it
/// into the internal representation (it may have been rescaled or
/// manipulated)
/// Enter or add value but also deal with count grid
virtual void value_input(std::vector<int> const &ix,
cvm::real const &new_value,
size_t const &imult = 0,
@ -1580,7 +1459,7 @@ public:
colvar_grid_gradient();
/// Destructor
virtual inline ~colvar_grid_gradient()
virtual ~colvar_grid_gradient()
{}
/// Constructor from specific sizes arrays
@ -1592,6 +1471,28 @@ public:
/// Constructor from a multicol file
colvar_grid_gradient(std::string &filename);
/// Read a grid written by write_multicol(), incrementin if data is true
virtual std::istream & read_multicol(std::istream &is, bool add = false);
/// Read a grid written by write_multicol(), incrementin if data is true
virtual int read_multicol(std::string const &filename,
std::string description = "grid file",
bool add = false);
/// Write grid in a format which is both human-readable and gnuplot-friendly
virtual std::ostream & write_multicol(std::ostream &os) const;
/// Write grid in a format which is both human-readable and gnuplot-friendly
virtual int write_multicol(std::string const &filename,
std::string description = "grid file") const;
/// Write the grid data without labels, as they are represented in memory
virtual std::ostream & write_opendx(std::ostream &os) const;
/// Write the grid data without labels, as they are represented in memory
virtual int write_opendx(std::string const &filename,
std::string description = "grid file") const;
/// \brief Get a vector with the binned value(s) indexed by ix, normalized if applicable
inline void vector_value(std::vector<int> const &ix, std::vector<cvm::real> &v) const
{
@ -1647,7 +1548,7 @@ public:
/// \brief Return the value of the function at ix divided by its
/// number of samples (if the count grid is defined)
virtual inline cvm::real value_output(std::vector<int> const &ix,
virtual cvm::real value_output(std::vector<int> const &ix,
size_t const &imult = 0) const
{
if (samples)
@ -1661,7 +1562,7 @@ public:
/// \brief Get the value from a formatted output and transform it
/// into the internal representation (it may have been rescaled or
/// manipulated)
virtual inline void value_input(std::vector<int> const &ix,
virtual void value_input(std::vector<int> const &ix,
cvm::real const &new_value,
size_t const &imult = 0,
bool add = false)

261
lib/colvars/colvargrid_def.h Normal file
View File

@ -0,0 +1,261 @@
// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
/// \file Definition of the more complex members of colvar_grid<> template
#ifndef COLVARGRID_DEF_H
#define COLVARGRID_DEF_H
#include <iostream>
#include <iomanip>
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "colvar.h"
#include "colvargrid.h"
template <class T>
std::istream & colvar_grid<T>::read_multicol(std::istream &is, bool add)
{
// Data in the header: nColvars, then for each
// xiMin, dXi, nPoints, periodic flag
std::string hash;
cvm::real lower, width, x;
size_t n, periodic_flag;
bool remap;
std::vector<T> new_value;
std::vector<int> nx_read;
std::vector<int> bin;
if ( cv.size() > 0 && cv.size() != nd ) {
cvm::error("Cannot read grid file: number of variables in file differs from number referenced by grid.\n");
return is;
}
if ( !(is >> hash) || (hash != "#") ) {
cvm::error("Error reading grid at position "+
cvm::to_str(static_cast<size_t>(is.tellg()))+
" in stream(read \"" + hash + "\")\n", COLVARS_INPUT_ERROR);
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(static_cast<size_t>(is.tellg()))+
" in stream(read \"" + hash + "\")\n");
return is;
}
is >> lower >> width >> nx_read[i] >> periodic_flag;
if ( (cvm::fabs(lower - lower_boundaries[i].real_value) > 1.0e-10) ||
(cvm::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;
}
template <class T>
int colvar_grid<T>::read_multicol(std::string const &filename,
std::string description,
bool add)
{
std::istream &is = cvm::main()->proxy->input_stream(filename, description);
if (!is) {
return COLVARS_FILE_ERROR;
}
if (colvar_grid<T>::read_multicol(is, add)) {
cvm::main()->proxy->close_input_stream(filename);
return COLVARS_OK;
}
return COLVARS_FILE_ERROR;
}
template <class T>
std::ostream & colvar_grid<T>::write_multicol(std::ostream &os) const
{
// Save the output formats
std::ios_base::fmtflags prev_flags(os.flags());
// Data in the header: nColvars, then for each
// xiMin, dXi, nPoints, periodic
os << std::setw(2) << "# " << nd << "\n";
// Write the floating numbers in full precision
os.setf(std::ios::scientific, std::ios::floatfield);
for (size_t i = 0; i < nd; i++) {
os << "# "
<< std::setw(cvm::cv_width) << std::setprecision(cvm::cv_prec) << lower_boundaries[i] << " "
<< std::setw(cvm::cv_width) << std::setprecision(cvm::cv_prec) << 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(cvm::cv_width) << std::setprecision(cvm::cv_prec)
<< bin_to_value_scalar(ix[i], i);
}
os << " ";
for (size_t imult = 0; imult < mult; imult++) {
os << " "
<< std::setw(cvm::cv_width) << std::setprecision(cvm::cv_prec)
<< value_output(ix, imult);
}
os << "\n";
}
// Restore the output formats
os.flags(prev_flags);
return os;
}
template <class T>
int colvar_grid<T>::write_multicol(std::string const &filename,
std::string description) const
{
int error_code = COLVARS_OK;
std::ostream &os = cvm::main()->proxy->output_stream(filename, description);
if (!os) {
return COLVARS_FILE_ERROR;
}
error_code |= colvar_grid<T>::write_multicol(os) ? COLVARS_OK :
COLVARS_FILE_ERROR;
cvm::main()->proxy->close_output_stream(filename);
return error_code;
}
template <class T>
std::ostream & colvar_grid<T>::write_opendx(std::ostream &os) const
{
// write the header
os << "object 1 class gridpositions counts";
size_t icv;
for (icv = 0; icv < num_variables(); icv++) {
os << " " << number_of_points(icv);
}
os << "\n";
os << "origin";
for (icv = 0; icv < num_variables(); icv++) {
os << " " << (lower_boundaries[icv].real_value + 0.5 * widths[icv]);
}
os << "\n";
for (icv = 0; icv < num_variables(); icv++) {
os << "delta";
for (size_t icv2 = 0; icv2 < num_variables(); icv2++) {
if (icv == icv2) os << " " << widths[icv];
else os << " " << 0.0;
}
os << "\n";
}
os << "object 2 class gridconnections counts";
for (icv = 0; icv < num_variables(); icv++) {
os << " " << number_of_points(icv);
}
os << "\n";
os << "object 3 class array type double rank 0 items "
<< number_of_points() << " data follows\n";
write_raw(os);
os << "object \"collective variables scalar field\" class field\n";
return os;
}
template <class T>
int colvar_grid<T>::write_opendx(std::string const &filename,
std::string description) const
{
int error_code = COLVARS_OK;
std::ostream &os = cvm::main()->proxy->output_stream(filename, description);
if (!os) {
return COLVARS_FILE_ERROR;
}
error_code |= colvar_grid<T>::write_opendx(os) ? COLVARS_OK :
COLVARS_FILE_ERROR;
cvm::main()->proxy->close_output_stream(filename);
return error_code;
}
#endif

251
lib/colvars/colvarmodule.cpp
View File

@ -7,7 +7,10 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <iostream>
#include <iomanip>
#include <sstream>
#include <fstream>
#include <cstring>
#include <vector>
#include <map>
@ -71,8 +74,6 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
depth_s = 0;
log_level_ = 10;
cv_traj_os = NULL;
xyz_reader_use_count = 0;
num_biases_types_used_ =
@ -132,8 +133,6 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
cv_traj_freq = 100;
restart_out_freq = proxy->default_restart_frequency();
// by default overwrite the existing trajectory file
cv_traj_append = false;
cv_traj_write_labels = true;
// Removes the need for proxy specializations to create this
@ -190,12 +189,12 @@ int colvarmodule::read_config_file(char const *config_filename)
std::string(config_filename)+"\":\n");
// open the configfile
config_s.open(config_filename);
if (!config_s.is_open()) {
cvm::error("Error: in opening configuration file \""+
std::istream &config_s = proxy->input_stream(config_filename,
"configuration file/string");
if (!config_s) {
return cvm::error("Error: in opening configuration file \""+
std::string(config_filename)+"\".\n",
COLVARS_FILE_ERROR);
return COLVARS_ERROR;
}
// read the config file into a string
@ -206,7 +205,7 @@ int colvarmodule::read_config_file(char const *config_filename)
if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
conf.append(line+"\n");
}
config_s.close();
proxy->close_input_stream(config_filename);
return parse_config(conf);
}
@ -299,9 +298,6 @@ int colvarmodule::parse_config(std::string &conf)
cvm::log("Collective variables module (re)initialized.\n");
cvm::log(cvm::line_marker);
// Update any necessary proxy data
proxy->setup();
if (source_Tcl_script.size() > 0) {
run_tcl_script(source_Tcl_script);
}
@ -385,10 +381,6 @@ int colvarmodule::parse_global_params(std::string const &conf)
parse->get_keyval(conf, "colvarsRestartFrequency",
restart_out_freq, restart_out_freq);
// Deprecate append flag
parse->get_keyval(conf, "colvarsTrajAppend",
cv_traj_append, cv_traj_append, colvarparse::parse_silent);
parse->get_keyval(conf, "scriptedColvarForces",
use_scripted_forces, use_scripted_forces);
@ -433,6 +425,7 @@ int colvarmodule::parse_colvars(std::string const &conf)
cvm::log("Error while constructing colvar number " +
cvm::to_str(colvars.size()) + " : deleting.");
delete colvars.back(); // the colvar destructor updates the colvars array
cvm::decrease_depth();
return COLVARS_ERROR;
}
cvm::decrease_depth();
@ -855,13 +848,15 @@ int colvarmodule::calc_colvars()
// so they can activate colvars as needed
std::vector<colvarbias *>::iterator bi;
for (bi = biases.begin(); bi != biases.end(); bi++) {
int tsf = (*bi)->get_time_step_factor();
if (tsf > 0 && (step_absolute() % tsf == 0)) {
int const tsf = (*bi)->get_time_step_factor();
if (tsf > 1) {
if (step_absolute() % tsf == 0) {
(*bi)->enable(colvardeps::f_cvb_awake);
} else {
(*bi)->disable(colvardeps::f_cvb_awake);
}
}
}
int error_code = COLVARS_OK;
std::vector<colvar *>::iterator cvi;
@ -870,13 +865,15 @@ int colvarmodule::calc_colvars()
variables_active()->clear();
variables_active()->reserve(variables()->size());
for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
// Wake up or put to sleep variables
// Wake up or put to sleep variables with MTS
int tsf = (*cvi)->get_time_step_factor();
if (tsf > 0 && (step_absolute() % tsf == 0)) {
if (tsf > 1) {
if (step_absolute() % tsf == 0) {
(*cvi)->enable(colvardeps::f_cv_awake);
} else {
(*cvi)->disable(colvardeps::f_cv_awake);
}
}
if ((*cvi)->is_enabled()) {
variables_active()->push_back(*cvi);
@ -1013,10 +1010,7 @@ int colvarmodule::update_colvar_forces()
cvm::log("Collecting forces from all biases.\n");
cvm::increase_depth();
for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
(*bi)->communicate_forces();
if (cvm::get_error()) {
return COLVARS_ERROR;
}
error_code |= (*bi)->communicate_forces();
}
cvm::decrease_depth();
@ -1040,9 +1034,6 @@ int colvarmodule::update_colvar_forces()
for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
// Inactive colvars will only reset their forces and return 0 energy
total_colvar_energy += (*cvi)->update_forces_energy();
if (cvm::get_error()) {
return COLVARS_ERROR;
}
}
cvm::decrease_depth();
if (cvm::debug())
@ -1064,7 +1055,7 @@ int colvarmodule::update_colvar_forces()
}
cvm::decrease_depth();
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
return error_code;
}
@ -1089,17 +1080,15 @@ int colvarmodule::calc_scripted_forces()
int colvarmodule::write_restart_file(std::string const &out_name)
{
cvm::log("Saving collective variables state to \""+out_name+"\".\n");
proxy->backup_file(out_name);
std::ostream *restart_out_os = proxy->output_stream(out_name);
if (!restart_out_os) return cvm::get_error();
if (!write_restart(*restart_out_os)) {
std::ostream &restart_out_os = proxy->output_stream(out_name, "state file");
if (!restart_out_os) return COLVARS_FILE_ERROR;
if (!write_restart(restart_out_os)) {
return cvm::error("Error: in writing restart file.\n", COLVARS_FILE_ERROR);
}
proxy->close_output_stream(out_name);
if (cv_traj_os != NULL) {
// Take the opportunity to flush colvars.traj
proxy->flush_output_stream(cv_traj_os);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -1118,38 +1107,46 @@ int colvarmodule::write_restart_string(std::string &output)
int colvarmodule::write_traj_files()
{
int error_code = COLVARS_OK;
if (cvm::debug()) {
cvm::log("colvarmodule::write_traj_files()\n");
}
if (cv_traj_os == NULL) {
if (open_traj_file(cv_traj_name) != COLVARS_OK) {
return cvm::get_error();
} else {
cv_traj_write_labels = true;
}
std::ostream &cv_traj_os = proxy->output_stream(cv_traj_name,
"colvars trajectory");
if (!cv_traj_os) {
return COLVARS_FILE_ERROR;
}
// write labels in the traj file every 1000 lines and at first timestep
if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 ||
cvm::step_relative() == 0 ||
cv_traj_write_labels) {
write_traj_label(*cv_traj_os);
}
// Write labels in the traj file at beginning and then every 1000 lines
if ( (cvm::step_relative() == 0) || cv_traj_write_labels ||
((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0) ) {
error_code |=
write_traj_label(cv_traj_os) ? COLVARS_OK : COLVARS_FILE_ERROR;
cv_traj_write_labels = false;
}
if (cvm::debug()) {
proxy->flush_output_stream(cv_traj_name);
}
if ((cvm::step_absolute() % cv_traj_freq) == 0) {
write_traj(*cv_traj_os);
error_code |= write_traj(cv_traj_os) ? COLVARS_OK : COLVARS_FILE_ERROR;
}
if (restart_out_freq && (cv_traj_os != NULL) &&
((cvm::step_absolute() % restart_out_freq) == 0)) {
if (cvm::debug()) {
proxy->flush_output_stream(cv_traj_name);
}
if (restart_out_freq && ((cvm::step_absolute() % restart_out_freq) == 0)) {
cvm::log("Synchronizing (emptying the buffer of) trajectory file \""+
cv_traj_name+"\".\n");
proxy->flush_output_stream(cv_traj_os);
error_code |= proxy->flush_output_stream(cv_traj_name);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
return error_code;
}
@ -1208,7 +1205,7 @@ int colvarmodule::end_of_step()
}
int colvarmodule::setup()
int colvarmodule::update_engine_parameters()
{
if (this->size() == 0) return cvm::get_error();
for (std::vector<colvar *>::iterator cvi = variables()->begin();
@ -1221,8 +1218,8 @@ int colvarmodule::setup()
colvarmodule::~colvarmodule()
{
if ((proxy->smp_thread_id() == COLVARS_NOT_IMPLEMENTED) ||
(proxy->smp_thread_id() == 0)) {
if ((proxy->smp_thread_id() < 0) || // not using threads
(proxy->smp_thread_id() == 0)) { // or this is thread 0
reset();
@ -1250,8 +1247,6 @@ colvarmodule::~colvarmodule()
int colvarmodule::reset()
{
cvm::log("Resetting the Collective Variables module.\n");
parse->clear();
// Iterate backwards because we are deleting the elements as we go
@ -1289,30 +1284,34 @@ int colvarmodule::setup_input()
// Read a state file
std::string restart_in_name(proxy->input_prefix()+
std::string(".colvars.state"));
std::ifstream input_is(restart_in_name.c_str());
if (!input_is.good()) {
// Try without the suffix
input_is.clear();
std::istream *input_is = &(proxy->input_stream(restart_in_name,
"restart file/channel",
false));
if (!*input_is) {
// Try without the suffix ".colvars.state"
restart_in_name = proxy->input_prefix();
input_is.open(restart_in_name.c_str());
input_is = &(proxy->input_stream(restart_in_name,
"restart file/channel"));
if (!*input_is) {
return COLVARS_FILE_ERROR;
}
}
// Now that the file has been opened, clear this for the next round
// Now that the file has been opened, clear this field so that this
// function will not be called twice
proxy->input_prefix().clear();
if (!input_is.good()) {
return cvm::error("Error: in opening input state file \""+
std::string(restart_in_name)+"\".\n",
COLVARS_FILE_ERROR);
} else {
cvm::log(cvm::line_marker);
cvm::log("Loading state from file \""+restart_in_name+"\".\n");
read_restart(input_is);
read_restart(*input_is);
cvm::log(cvm::line_marker);
proxy->close_input_stream(restart_in_name);
return cvm::get_error();
}
}
// TODO This could soon be redundant
if (proxy->input_buffer() != NULL) {
// Read a string buffer
char const *buffer = proxy->input_buffer();
@ -1364,10 +1363,6 @@ int colvarmodule::setup_output()
std::string(output_prefix()+".colvars.traj") :
std::string(""));
if (cv_traj_freq && cv_traj_name.size()) {
error_code |= open_traj_file(cv_traj_name);
}
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
@ -1572,7 +1567,7 @@ int colvarmodule::write_output_files()
error_code |= (*bi)->write_state_to_replicas();
}
cvm::decrease_depth();
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
return error_code;
}
@ -1582,6 +1577,9 @@ int colvarmodule::read_traj(char const *traj_filename,
{
cvm::log("Opening trajectory file \""+
std::string(traj_filename)+"\".\n");
// NB: this function is not currently used, but when it will it should
// retain the ability for direct file-based access (in case traj files
// exceed memory)
std::ifstream traj_is(traj_filename);
while (true) {
@ -1683,42 +1681,6 @@ std::ostream & colvarmodule::write_restart(std::ostream &os)
}
int colvarmodule::open_traj_file(std::string const &file_name)
{
if (cv_traj_os != NULL) {
return COLVARS_OK;
}
// (re)open trajectory file
if (cv_traj_append) {
cvm::log("Appending to trajectory file \""+file_name+"\".\n");
cv_traj_os = (cvm::proxy)->output_stream(file_name, std::ios::app);
} else {
cvm::log("Opening trajectory file \""+file_name+"\".\n");
proxy->backup_file(file_name.c_str());
cv_traj_os = (cvm::proxy)->output_stream(file_name);
}
if (cv_traj_os == NULL) {
cvm::error("Error: cannot write to file \""+file_name+"\".\n",
COLVARS_FILE_ERROR);
}
return cvm::get_error();
}
int colvarmodule::close_traj_file()
{
if (cv_traj_os != NULL) {
cvm::log("Closing trajectory file \""+cv_traj_name+"\".\n");
proxy->close_output_stream(cv_traj_name);
cv_traj_os = NULL;
}
return cvm::get_error();
}
std::ostream & colvarmodule::write_traj_label(std::ostream &os)
{
os.setf(std::ios::scientific, std::ios::floatfield);
@ -1739,10 +1701,6 @@ std::ostream & colvarmodule::write_traj_label(std::ostream &os)
}
os << "\n";
if (cvm::debug()) {
proxy->flush_output_stream(&os);
}
cvm::decrease_depth();
return os;
}
@ -1768,10 +1726,6 @@ std::ostream & colvarmodule::write_traj(std::ostream &os)
}
os << "\n";
if (cvm::debug()) {
proxy->flush_output_stream(&os);
}
cvm::decrease_depth();
return os;
}
@ -1780,12 +1734,15 @@ std::ostream & colvarmodule::write_traj(std::ostream &os)
void colvarmodule::log(std::string const &message, int min_log_level)
{
if (cvm::log_level() < min_log_level) return;
std::string const trailing_newline = (message.size() > 0) ?
(message[message.size()-1] == '\n' ? "" : "\n") : "";
// allow logging when the module is not fully initialized
size_t const d = (cvm::main() != NULL) ? depth() : 0;
if (d > 0) {
proxy->log((std::string(2*d, ' '))+message);
proxy->log((std::string(2*d, ' ')) + message + trailing_newline);
} else {
proxy->log(message);
proxy->log(message + trailing_newline);
}
}
@ -1854,18 +1811,26 @@ void colvarmodule::clear_error()
int colvarmodule::error(std::string const &message, int code)
{
set_error_bits(code);
proxy->error(message);
std::string const trailing_newline = (message.size() > 0) ?
(message[message.size()-1] == '\n' ? "" : "\n") : "";
size_t const d = depth();
if (d > 0) {
proxy->error((std::string(2*d, ' ')) + message + trailing_newline);
} else {
proxy->error(message + trailing_newline);
}
return get_error();
}
int cvm::read_index_file(char const *filename)
{
std::ifstream is(filename, std::ios::binary);
if (!is.good()) {
return cvm::error("Error: in opening index file \""+
std::string(filename)+"\".\n",
COLVARS_FILE_ERROR);
std::istream &is = proxy->input_stream(filename, "index file");
if (!is) {
return COLVARS_FILE_ERROR;
} else {
index_file_names.push_back(std::string(filename));
}
@ -1947,7 +1912,7 @@ int cvm::read_index_file(char const *filename)
cvm::to_str((index_groups[i])->size())+" atoms)\n");
}
return COLVARS_OK;
return proxy->close_input_stream(filename);
}
@ -2016,9 +1981,10 @@ int cvm::load_coords(char const *file_name,
int cvm::load_coords_xyz(char const *filename,
std::vector<rvector> *pos,
cvm::atom_group *atoms)
cvm::atom_group *atoms,
bool keep_open)
{
std::ifstream xyz_is(filename);
std::istream &xyz_is = proxy->input_stream(filename, "XYZ file");
unsigned int natoms;
char symbol[256];
std::string line;
@ -2028,7 +1994,8 @@ int cvm::load_coords_xyz(char const *filename,
std::string(filename)+"\".\n");
if ( ! (xyz_is >> natoms) ) {
return cvm::error(error_msg, COLVARS_INPUT_ERROR);
// Return silent error when reaching the end of multi-frame files
return keep_open ? COLVARS_NO_SUCH_FRAME : cvm::error(error_msg, COLVARS_INPUT_ERROR);
}
++xyz_reader_use_count;
@ -2049,6 +2016,12 @@ int cvm::load_coords_xyz(char const *filename,
size_t xyz_natoms = 0;
if (pos->size() != natoms) { // Use specified indices
int next = 0; // indices are zero-based
if (!atoms) {
// In the other branch of this test, reading all positions from the file,
// a valid atom group pointer is not necessary
return cvm::error("Trying to read partial positions with invalid atom group pointer",
COLVARS_BUG_ERROR);
}
std::vector<int>::const_iterator index = atoms->sorted_ids().begin();
for ( ; pos_i != pos->end() ; pos_i++, index++) {
@ -2092,7 +2065,11 @@ int cvm::load_coords_xyz(char const *filename,
cvm::to_str(pos->size())+".\n", COLVARS_INPUT_ERROR);
}
if (keep_open) {
return COLVARS_OK;
} else {
return proxy->close_input_stream(filename);
}
}
@ -2100,18 +2077,6 @@ int cvm::load_coords_xyz(char const *filename,
// Wrappers to proxy functions: these may go in the future
cvm::real cvm::boltzmann()
{
return proxy->boltzmann();
}
cvm::real cvm::temperature()
{
return proxy->temperature();
}
cvm::real cvm::dt()
{
return proxy->dt();

26
lib/colvars/colvarmodule.h
View File

@ -42,13 +42,11 @@ You can browse the class hierarchy or the list of source files.
#define COLVARS_MEMORY_ERROR (1<<5)
#define COLVARS_NO_SUCH_FRAME (1<<6) // Cannot load the requested frame
#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <string>
#include <vector>
#include <list>
#include <iosfwd>
class colvarparse;
class colvar;
@ -441,9 +439,9 @@ public:
// 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)
/// (Re)initialize any internal data affected by changes in the engine
/// Also calls setup() member functions of colvars and biases
int setup();
int update_engine_parameters();
/// (Re)initialize and (re)read the input state file calling read_restart()
int setup_input();
@ -634,12 +632,6 @@ public:
// proxy functions
/// \brief Boltmann constant
static real boltzmann();
/// \brief Temperature of the simulation (K)
static real temperature();
/// \brief Time step of MD integrator (fs)
static real dt();
@ -751,7 +743,8 @@ public:
/// Load coordinates into an atom group from an XYZ file (assumes Angstroms)
int load_coords_xyz(char const *filename,
std::vector<rvector> *pos,
atom_group *atoms);
atom_group *atoms,
bool keep_open = false);
/// Frequency for collective variables trajectory output
static size_t cv_traj_freq;
@ -766,21 +759,12 @@ public:
protected:
/// Configuration file
std::ifstream config_s;
/// Configuration file parser object
colvarparse *parse;
/// Name of the trajectory file
std::string cv_traj_name;
/// Collective variables output trajectory file
std::ostream *cv_traj_os;
/// Appending to the existing trajectory file?
bool cv_traj_append;
/// Write labels at the next iteration
bool cv_traj_write_labels;

46
lib/colvars/colvarmodule_refs.h
View File

@ -63,6 +63,22 @@
" url = {https://doi.org/10.1021/ct500874p}\n"
"}\n";
paper_count_[std::string("Ebrahimi2022")] = 0;
paper_url_[std::string("Ebrahimi2022")] = "https://doi.org/10.1021/acs.jctc.1c01235";
paper_bibtex_[std::string("Ebrahimi2022")] =
"\n"
"@article {Ebrahimi2022,\n"
" author = {Ebrahimi, Mina and H\\'enin, J\\'er\\^ome},\n"
" title = {Symmetry-Adapted Restraints for Binding Free Energy Calculations},\n"
" journal = {Journal of Chemical Theory and Computation},\n"
" volume = {18},\n"
" number = {4},\n"
" pages = {2494-2502},\n"
" year = {2022},\n"
" doi = {10.1021/acs.jctc.1c01235},\n"
" url = {https://doi.org/10.1021/acs.jctc.1c01235}\n"
"}\n";
paper_count_[std::string("Fiorin2013")] = 0;
paper_url_[std::string("Fiorin2013")] = "https://doi.org/10.1080/00268976.2013.813594";
paper_bibtex_[std::string("Fiorin2013")] =
@ -246,20 +262,19 @@
" url = {https://doi.org/10.1063/5.0014475}\n"
"}\n";
paper_count_[std::string("Plimpton1995")] = 0;
paper_url_[std::string("Plimpton1995")] = "https://doi.org/10.1006/jcph.1995.1039";
paper_bibtex_[std::string("Plimpton1995")] =
paper_count_[std::string("Thompson2022")] = 0;
paper_url_[std::string("Thompson2022")] = "https://doi.org/10.1016/j.cpc.2021.108171";
paper_bibtex_[std::string("Thompson2022")] =
"\n"
"@article{Plimpton1995,\n"
" title = {Fast parallel algorithms for short-range molecular dynamics},\n"
" author = {Plimpton, Steve},\n"
" journal = {J. Comp. Phys.},\n"
" year = {1995},\n"
" volume = {117},\n"
" number = {1},\n"
" pages = {1--19},\n"
" doi = {10.1006/jcph.1995.1039},\n"
" url = {https://doi.org/10.1006/jcph.1995.1039}\n"
"@article{Thompson2022,\n"
" title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},\n"
" author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},\n"
" journal = {Comp. Phys. Comm.},\n"
" volume = {271},\n"
" pages = {108171},\n"
" year = {2022},\n"
" doi = {10.1016/j.cpc.2021.108171},\n"
" url = {https://doi.org/10.1016/j.cpc.2021.108171}\n"
"}\n";
paper_count_[std::string("Shen2015")] = 0;
@ -329,6 +344,9 @@
feature_count_[std::string("Multiple-walker ABF implementation")] = 0;
feature_paper_map_[std::string("Multiple-walker ABF implementation")] = "Comer2014c";
feature_count_[std::string("Symmetry-adapted RMSD")] = 0;
feature_paper_map_[std::string("Symmetry-adapted RMSD")] = "Ebrahimi2022";
feature_count_[std::string("Colvars module")] = 0;
feature_paper_map_[std::string("Colvars module")] = "Fiorin2013";
@ -504,7 +522,7 @@
feature_paper_map_[std::string("Scalable center-of-mass computation (NAMD)")] = "Phillips2020";
feature_count_[std::string("LAMMPS engine")] = 0;
feature_paper_map_[std::string("LAMMPS engine")] = "Plimpton1995";
feature_paper_map_[std::string("LAMMPS engine")] = "Thompson2022";
feature_count_[std::string("distancePairs colvar component")] = 0;
feature_paper_map_[std::string("distancePairs colvar component")] = "Shen2015";

537
lib/colvars/colvarproxy.cpp
View File

@ -7,23 +7,9 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
// Using access() to check if a file exists (until we can assume C++14/17)
#if !defined(_WIN32) || defined(__CYGWIN__)
#include <unistd.h>
#endif
#if defined(_WIN32)
#include <io.h>
#endif
#include <cerrno>
#include <sstream>
#include <cstring>
#include <cstdio>
#if defined(_OPENMP)
#include <omp.h>
#endif
#include <fstream>
#include <list>
#include <utility>
#include "colvarmodule.h"
#include "colvarproxy.h"
@ -33,205 +19,6 @@
colvarproxy_system::colvarproxy_system()
{
angstrom_value = 0.0;
kcal_mol_value = 0.0;
boundaries_type = boundaries_unsupported;
total_force_requested = false;
indirect_lambda_biasing_force = 0.0;
cached_alch_lambda_changed = false;
cached_alch_lambda = -1.0;
reset_pbc_lattice();
}
colvarproxy_system::~colvarproxy_system() {}
int colvarproxy_system::set_unit_system(std::string const & /* units */,
bool /* check_only */)
{
return COLVARS_NOT_IMPLEMENTED;
}
cvm::real colvarproxy_system::backend_angstrom_value()
{
return 1.0;
}
cvm::real colvarproxy_system::boltzmann()
{
return 0.001987191;
}
cvm::real colvarproxy_system::temperature()
{
// TODO define, document and implement a user method to set the value of this
return 300.0;
}
cvm::real colvarproxy_system::dt()
{
// TODO define, document and implement a user method to set the value of this
return 1.0;
}
cvm::real colvarproxy_system::rand_gaussian()
{
// TODO define, document and implement a user method to set the value of this
return 0.0;
}
void colvarproxy_system::add_energy(cvm::real /* energy */) {}
void colvarproxy_system::request_total_force(bool yesno)
{
if (yesno == true)
cvm::error("Error: total forces are currently not implemented.\n",
COLVARS_NOT_IMPLEMENTED);
}
bool colvarproxy_system::total_forces_enabled() const
{
return false;
}
bool colvarproxy_system::total_forces_same_step() const
{
return false;
}
inline int round_to_integer(cvm::real x)
{
return int(cvm::floor(x+0.5));
}
void colvarproxy_system::update_pbc_lattice()
{
// Periodicity is assumed in all directions
if (boundaries_type == boundaries_unsupported ||
boundaries_type == boundaries_non_periodic) {
cvm::error("Error: setting PBC lattice with unsupported boundaries.\n",
COLVARS_BUG_ERROR);
return;
}
{
cvm::rvector const v = cvm::rvector::outer(unit_cell_y, unit_cell_z);
reciprocal_cell_x = v/(v*unit_cell_x);
}
{
cvm::rvector const v = cvm::rvector::outer(unit_cell_z, unit_cell_x);
reciprocal_cell_y = v/(v*unit_cell_y);
}
{
cvm::rvector const v = cvm::rvector::outer(unit_cell_x, unit_cell_y);
reciprocal_cell_z = v/(v*unit_cell_z);
}
}
void colvarproxy_system::reset_pbc_lattice()
{
unit_cell_x.reset();
unit_cell_y.reset();
unit_cell_z.reset();
reciprocal_cell_x.reset();
reciprocal_cell_y.reset();
reciprocal_cell_z.reset();
}
cvm::rvector colvarproxy_system::position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
const
{
if (boundaries_type == boundaries_unsupported) {
cvm::error("Error: unsupported boundary conditions.\n", COLVARS_INPUT_ERROR);
}
cvm::rvector diff = (pos2 - pos1);
if (boundaries_type == boundaries_non_periodic) return diff;
cvm::real const x_shift = round_to_integer(reciprocal_cell_x*diff);
cvm::real const y_shift = round_to_integer(reciprocal_cell_y*diff);
cvm::real const z_shift = round_to_integer(reciprocal_cell_z*diff);
diff.x -= x_shift*unit_cell_x.x + y_shift*unit_cell_y.x +
z_shift*unit_cell_z.x;
diff.y -= x_shift*unit_cell_x.y + y_shift*unit_cell_y.y +
z_shift*unit_cell_z.y;
diff.z -= x_shift*unit_cell_x.z + y_shift*unit_cell_y.z +
z_shift*unit_cell_z.z;
return diff;
}
int colvarproxy_system::get_molid(int &)
{
cvm::error("Error: only VMD allows the use of multiple \"molecules\", "
"i.e. multiple molecular systems.", COLVARS_NOT_IMPLEMENTED);
return -1;
}
int colvarproxy_system::get_alch_lambda(cvm::real * /* lambda */)
{
return cvm::error("Error in get_alch_lambda: alchemical lambda dynamics is not supported by this build.",
COLVARS_NOT_IMPLEMENTED);
}
void colvarproxy_system::set_alch_lambda(cvm::real lambda)
{
cached_alch_lambda = lambda;
cached_alch_lambda_changed = true;
}
int colvarproxy_system::send_alch_lambda()
{
return cvm::error("Error in set_alch_lambda: alchemical lambda dynamics is not supported by this build.",
COLVARS_NOT_IMPLEMENTED);
}
int colvarproxy_system::get_dE_dlambda(cvm::real * /* force */)
{
return cvm::error("Error in get_dE_dlambda: alchemical lambda dynamics is not supported by this build.",
COLVARS_NOT_IMPLEMENTED);
}
int colvarproxy_system::apply_force_dE_dlambda(cvm::real* /* force */)
{
return cvm::error("Error in apply_force_dE_dlambda: function is not implemented by this build.",
COLVARS_NOT_IMPLEMENTED);
}
int colvarproxy_system::get_d2E_dlambda2(cvm::real*)
{
return cvm::error("Error in get_d2E_dlambda2: function is not implemented by this build.",
COLVARS_NOT_IMPLEMENTED);
}
colvarproxy_atoms::colvarproxy_atoms()
{
atoms_rms_applied_force_ = atoms_max_applied_force_ = 0.0;
@ -249,7 +36,7 @@ colvarproxy_atoms::~colvarproxy_atoms()
int colvarproxy_atoms::reset()
{
atoms_ids.clear();
atoms_ncopies.clear();
atoms_refcount.clear();
atoms_masses.clear();
atoms_charges.clear();
atoms_positions.clear();
@ -262,7 +49,7 @@ int colvarproxy_atoms::reset()
int colvarproxy_atoms::add_atom_slot(int atom_id)
{
atoms_ids.push_back(atom_id);
atoms_ncopies.push_back(1);
atoms_refcount.push_back(1);
atoms_masses.push_back(1.0);
atoms_charges.push_back(0.0);
atoms_positions.push_back(cvm::rvector(0.0, 0.0, 0.0));
@ -309,12 +96,22 @@ void colvarproxy_atoms::clear_atom(int index)
cvm::error("Error: trying to disable an atom that was not previously requested.\n",
COLVARS_INPUT_ERROR);
}
if (atoms_ncopies[index] > 0) {
atoms_ncopies[index] -= 1;
if (atoms_refcount[index] > 0) {
atoms_refcount[index] -= 1;
}
}
size_t colvarproxy_atoms::get_num_active_atoms() const
{
size_t result = 0;
for (size_t i = 0; i < atoms_refcount.size(); i++) {
if (atoms_refcount[i] > 0) result++;
}
return result;
}
int colvarproxy_atoms::load_atoms(char const * /* filename */,
cvm::atom_group & /* atoms */,
std::string const & /* pdb_field */,
@ -382,7 +179,7 @@ colvarproxy_atom_groups::~colvarproxy_atom_groups()
int colvarproxy_atom_groups::reset()
{
atom_groups_ids.clear();
atom_groups_ncopies.clear();
atom_groups_refcount.clear();
atom_groups_masses.clear();
atom_groups_charges.clear();
atom_groups_coms.clear();
@ -395,7 +192,7 @@ int colvarproxy_atom_groups::reset()
int colvarproxy_atom_groups::add_atom_group_slot(int atom_group_id)
{
atom_groups_ids.push_back(atom_group_id);
atom_groups_ncopies.push_back(1);
atom_groups_refcount.push_back(1);
atom_groups_masses.push_back(1.0);
atom_groups_charges.push_back(0.0);
atom_groups_coms.push_back(cvm::rvector(0.0, 0.0, 0.0));
@ -427,12 +224,22 @@ void colvarproxy_atom_groups::clear_atom_group(int index)
"that was not previously requested.\n",
COLVARS_INPUT_ERROR);
}
if (atom_groups_ncopies[index] > 0) {
atom_groups_ncopies[index] -= 1;
if (atom_groups_refcount[index] > 0) {
atom_groups_refcount[index] -= 1;
}
}
size_t colvarproxy_atom_groups::get_num_active_atom_groups() const
{
size_t result = 0;
for (size_t i = 0; i < atom_groups_refcount.size(); i++) {
if (atom_groups_refcount[i] > 0) result++;
}
return result;
}
void colvarproxy_atom_groups::compute_rms_atom_groups_applied_force()
{
atom_groups_rms_applied_force_ =
@ -454,8 +261,8 @@ colvarproxy_smp::colvarproxy_smp()
omp_lock_state = NULL;
#if defined(_OPENMP)
if (omp_get_thread_num() == 0) {
omp_lock_state = reinterpret_cast<void *>(new omp_lock_t);
omp_init_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
omp_lock_state = new omp_lock_t;
omp_init_lock(omp_lock_state);
}
#endif
}
@ -466,7 +273,7 @@ colvarproxy_smp::~colvarproxy_smp()
#if defined(_OPENMP)
if (omp_get_thread_num() == 0) {
if (omp_lock_state) {
delete reinterpret_cast<omp_lock_t *>(omp_lock_state);
delete omp_lock_state;
}
}
#endif
@ -567,7 +374,7 @@ int colvarproxy_smp::smp_thread_id()
#if defined(_OPENMP)
return omp_get_thread_num();
#else
return COLVARS_NOT_IMPLEMENTED;
return -1;
#endif
}
@ -577,7 +384,7 @@ int colvarproxy_smp::smp_num_threads()
#if defined(_OPENMP)
return omp_get_max_threads();
#else
return COLVARS_NOT_IMPLEMENTED;
return -1;
#endif
}
@ -585,7 +392,7 @@ int colvarproxy_smp::smp_num_threads()
int colvarproxy_smp::smp_lock()
{
#if defined(_OPENMP)
omp_set_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
omp_set_lock(omp_lock_state);
#endif
return COLVARS_OK;
}
@ -594,8 +401,7 @@ int colvarproxy_smp::smp_lock()
int colvarproxy_smp::smp_trylock()
{
#if defined(_OPENMP)
return omp_test_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state)) ?
COLVARS_OK : COLVARS_ERROR;
return omp_test_lock(omp_lock_state) ? COLVARS_OK : COLVARS_ERROR;
#else
return COLVARS_OK;
#endif
@ -605,7 +411,7 @@ int colvarproxy_smp::smp_trylock()
int colvarproxy_smp::smp_unlock()
{
#if defined(_OPENMP)
omp_unset_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
omp_unset_lock(omp_lock_state);
#endif
return COLVARS_OK;
}
@ -651,151 +457,35 @@ int colvarproxy_script::run_colvar_gradient_callback(std::string const & /* name
colvarproxy_io::colvarproxy_io()
{
input_buffer_ = NULL;
restart_frequency_engine = 0;
}
colvarproxy_io::~colvarproxy_io() {}
int colvarproxy_io::get_frame(long int&)
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_io::set_frame(long int)
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_io::backup_file(char const *filename)
{
// Simplified version of NAMD_file_exists()
int exit_code;
do {
#if defined(_WIN32) && !defined(__CYGWIN__)
// We could use _access_s here, but it is probably too new
exit_code = _access(filename, 00);
#else
exit_code = access(filename, F_OK);
#endif
} while ((exit_code != 0) && (errno == EINTR));
if (exit_code != 0) {
if (errno == ENOENT) {
// File does not exist
return COLVARS_OK;
} else {
return cvm::error("Unknown error while checking if file \""+
std::string(filename)+"\" exists.\n", COLVARS_ERROR);
}
}
// The file exists, then rename it
if (std::string(filename).rfind(std::string(".colvars.state")) !=
std::string::npos) {
return rename_file(filename, (std::string(filename)+".old").c_str());
} else {
return rename_file(filename, (std::string(filename)+".BAK").c_str());
}
}
int colvarproxy_io::remove_file(char const *filename)
{
int error_code = COLVARS_OK;
#if defined(_WIN32) && !defined(__CYGWIN__)
// Because the file may be open by other processes, rename it to filename.old
std::string const renamed_file(std::string(filename)+".old");
// It may still be there from an interrupted run, so remove it to be safe
std::remove(renamed_file.c_str());
int rename_exit_code = 0;
while ((rename_exit_code = std::rename(filename,
renamed_file.c_str())) != 0) {
if (errno == EINTR) continue;
error_code |= COLVARS_FILE_ERROR;
break;
}
// Ask to remove filename.old, but ignore any errors raised
std::remove(renamed_file.c_str());
#else
if (std::remove(filename)) {
if (errno != ENOENT) {
error_code |= COLVARS_FILE_ERROR;
}
}
#endif
if (error_code != COLVARS_OK) {
return cvm::error("Error: in removing file \""+std::string(filename)+
"\".\n.",
error_code);
}
return COLVARS_OK;
}
int colvarproxy_io::rename_file(char const *filename, char const *newfilename)
{
int error_code = COLVARS_OK;
#if defined(_WIN32) && !defined(__CYGWIN__)
// On straight Windows, must remove the destination before renaming it
error_code |= remove_file(newfilename);
#endif
int rename_exit_code = 0;
while ((rename_exit_code = std::rename(filename, newfilename)) != 0) {
if (errno == EINTR) continue;
// Call log() instead of error to allow the next try
cvm::log("Error: in renaming file \""+std::string(filename)+"\" to \""+
std::string(newfilename)+"\".\n.");
error_code |= COLVARS_FILE_ERROR;
if (errno == EXDEV) continue;
break;
}
return rename_exit_code ? error_code : COLVARS_OK;
}
colvarproxy::colvarproxy()
{
colvars = NULL;
// By default, simulation engines allow to immediately request atoms
engine_ready_ = true;
b_simulation_running = true;
b_simulation_continuing = false;
b_delete_requested = false;
version_int = -1;
features_hash = 0;
config_queue_ = reinterpret_cast<void *>(new std::list<std::pair<std::string, std::string> >);
}
colvarproxy::~colvarproxy()
{
close_files();
close_output_streams();
if (colvars != NULL) {
delete colvars;
colvars = NULL;
}
delete reinterpret_cast<std::list<std::pair<std::string, std::string> > *>(config_queue_);
}
int colvarproxy::close_files()
bool colvarproxy::io_available()
{
if (smp_enabled() == COLVARS_OK && smp_thread_id() > 0) {
// Nothing to do on non-master threads
return COLVARS_OK;
}
std::list<std::string>::iterator osni = output_stream_names.begin();
std::list<std::ostream *>::iterator osi = output_files.begin();
for ( ; osi != output_files.end(); osi++, osni++) {
((std::ofstream *) (*osi))->close();
delete *osi;
}
output_files.clear();
output_stream_names.clear();
return COLVARS_OK;
return (smp_enabled() == COLVARS_OK && smp_thread_id() == 0) ||
(smp_enabled() != COLVARS_OK);
}
@ -816,12 +506,41 @@ int colvarproxy::request_deletion()
}
void colvarproxy::add_config(std::string const &cmd, std::string const &conf)
{
reinterpret_cast<std::list<std::pair<std::string, std::string> > *>(config_queue_)->push_back(std::make_pair(cmd, conf));
}
int colvarproxy::setup()
{
return COLVARS_OK;
}
int colvarproxy::parse_module_config()
{
int error_code = COLVARS_OK;
// Read any configuration queued up for Colvars
std::list<std::pair<std::string, std::string> > *config_queue = reinterpret_cast<std::list<std::pair<std::string, std::string> > *>(config_queue_);
while (config_queue->size() > 0) {
std::pair<std::string, std::string> const &p = config_queue->front();
if (p.first == "config") {
error_code |= colvars->read_config_string(p.second);
} else if (p.first == "configfile") {
error_code |= colvars->read_config_file(p.second.c_str());
} else {
error_code |= cvm::error(std::string("Error: invalid keyword \"") +
p.first +
std::string("\" in colvarproxy::setup()\n"),
COLVARS_BUG_ERROR);
}
config_queue->pop_front();
}
return error_code;
}
int colvarproxy::update_input()
{
return COLVARS_OK;
@ -874,7 +593,7 @@ void colvarproxy::print_input_atomic_data()
cvm::log("Step "+cvm::to_str(cvm::step_absolute())+", "+
"atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
cvm::log("Step "+cvm::to_str(cvm::step_absolute())+", "+
"atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n");
"atoms_refcount = "+cvm::to_str(atoms_refcount)+"\n");
cvm::log("Step "+cvm::to_str(cvm::step_absolute())+", "+
"atoms_masses = "+cvm::to_str(atoms_masses)+"\n");
cvm::log("Step "+cvm::to_str(cvm::step_absolute())+", "+
@ -893,7 +612,7 @@ void colvarproxy::print_input_atomic_data()
cvm::log("Step "+cvm::to_str(cvm::step_absolute())+", "+
"atom_groups_ids = "+cvm::to_str(atom_groups_ids)+"\n");
cvm::log("Step "+cvm::to_str(cvm::step_absolute())+", "+
"atom_groups_ncopies = "+cvm::to_str(atom_groups_ncopies)+"\n");
"atom_groups_refcount = "+cvm::to_str(atom_groups_refcount)+"\n");
cvm::log("Step "+cvm::to_str(cvm::step_absolute())+", "+
"atom_groups_masses = "+cvm::to_str(atom_groups_masses)+"\n");
cvm::log("Step "+cvm::to_str(cvm::step_absolute())+", "+
@ -988,103 +707,3 @@ int colvarproxy::get_version_from_string(char const *version_string)
}
void colvarproxy::smp_stream_error()
{
cvm::error("Error: trying to access an output stream from a "
"multi-threaded region (bug). For a quick workaround, use "
"\"smp off\" in the Colvars config.\n", COLVARS_BUG_ERROR);
}
std::ostream * colvarproxy::output_stream(std::string const &output_name,
std::ios_base::openmode mode)
{
if (cvm::debug()) {
cvm::log("Using colvarproxy::output_stream()\n");
}
std::ostream *os = get_output_stream(output_name);
if (os != NULL) return os;
if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
backup_file(output_name);
}
std::ofstream *osf = new std::ofstream(output_name.c_str(), mode);
if (!osf->is_open()) {
cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
COLVARS_FILE_ERROR);
return NULL;
}
output_stream_names.push_back(output_name);
output_files.push_back(osf);
return osf;
}
std::ostream *colvarproxy::get_output_stream(std::string const &output_name)
{
if (smp_enabled() == COLVARS_OK) {
if (smp_thread_id() > 0) smp_stream_error();
}
std::list<std::ostream *>::iterator osi = output_files.begin();
std::list<std::string>::iterator osni = output_stream_names.begin();
for ( ; osi != output_files.end(); osi++, osni++) {
if (*osni == output_name) {
return *osi;
}
}
return NULL;
}
int colvarproxy::flush_output_stream(std::ostream *os)
{
if (smp_enabled() == COLVARS_OK) {
if (smp_thread_id() > 0) smp_stream_error();
}
std::list<std::ostream *>::iterator osi = output_files.begin();
std::list<std::string>::iterator osni = output_stream_names.begin();
for ( ; osi != output_files.end(); osi++, osni++) {
if (*osi == os) {
((std::ofstream *) (*osi))->flush();
return COLVARS_OK;
}
}
return cvm::error("Error: trying to flush an output file/channel "
"that wasn't open.\n", COLVARS_BUG_ERROR);
}
int colvarproxy::flush_output_streams()
{
if (smp_enabled() == COLVARS_OK && smp_thread_id() > 0)
return COLVARS_OK;
std::list<std::ostream *>::iterator osi = output_files.begin();
for ( ; osi != output_files.end(); osi++) {
((std::ofstream *) (*osi))->flush();
}
return COLVARS_OK;
}
int colvarproxy::close_output_stream(std::string const &output_name)
{
if (smp_enabled() == COLVARS_OK) {
if (smp_thread_id() > 0) smp_stream_error();
}
std::list<std::ostream *>::iterator osi = output_files.begin();
std::list<std::string>::iterator osni = output_stream_names.begin();
for ( ; osi != output_files.end(); osi++, osni++) {
if (*osni == output_name) {
((std::ofstream *) (*osi))->close();
delete *osi;
output_files.erase(osi);
output_stream_names.erase(osni);
return COLVARS_OK;
}
}
return cvm::error("Error: trying to close an output file/channel "
"that wasn't open.\n", COLVARS_BUG_ERROR);
}

352
lib/colvars/colvarproxy.h
View File

@ -10,12 +10,11 @@
#ifndef COLVARPROXY_H
#define COLVARPROXY_H
#include <fstream>
#include <list>
#include "colvarmodule.h"
#include "colvartypes.h"
#include "colvarvalue.h"
#include "colvarproxy_io.h"
#include "colvarproxy_system.h"
#include "colvarproxy_tcl.h"
#include "colvarproxy_volmaps.h"
@ -38,165 +37,6 @@
class colvarscript;
/// Methods for accessing the simulation system (PBCs, integrator, etc)
class colvarproxy_system {
public:
/// Constructor
colvarproxy_system();
/// Destructor
virtual ~colvarproxy_system();
/// \brief Name of the unit system used internally by Colvars (by default, that of the back-end).
/// Supported depending on the back-end: real (A, kcal/mol), metal (A, eV), electron (Bohr, Hartree), gromacs (nm, kJ/mol)
/// Note: calls to back-end PBC functions assume back-end length unit
/// We use different unit from back-end in VMD bc using PBC functions from colvarproxy base class
/// Colvars internal units are user specified, because the module exchanges info in unknown
/// composite dimensions with user input, while it only exchanges quantities of known
/// dimension with the back-end (length and forces)
std::string units;
/// \brief Request to set the units used internally by Colvars
virtual int set_unit_system(std::string const &units, bool check_only);
/// \brief Value of 1 Angstrom in the internal (front-end) Colvars unit for atomic coordinates
/// * defaults to 0. in the base class; derived proxy classes must set it
/// * in VMD proxy, can only be changed when no variables are defined
/// as user-defined values in composite units must be compatible with that system
cvm::real angstrom_value;
/// \brief Value of 1 Angstrom in the backend's unit for atomic coordinates
virtual cvm::real backend_angstrom_value();
/// \brief Value of 1 kcal/mol in the internal Colvars unit for energy
cvm::real kcal_mol_value;
/// \brief Convert a length from Angstrom to internal
inline cvm::real angstrom_to_internal(cvm::real l) const
{
return l * angstrom_value;
}
/// \brief Convert a length from internal to Angstrom
inline cvm::real internal_to_angstrom(cvm::real l) const
{
return l / angstrom_value;
}
// /// \brief Convert a length from back-end unit to internal
// inline cvm::real back_end_to_internal_unit(cvm::real l) {
// if (angstrom_value == 0.) {
// return l / backend_angstrom_value();
// }
// return l * angstrom_value / backend_angstrom_value();
// }
/// \brief Boltzmann constant in internal Colvars units
virtual cvm::real boltzmann();
/// \brief Target temperature of the simulation (K units)
virtual cvm::real temperature();
/// \brief Time step of the simulation (fs)
virtual cvm::real dt();
/// \brief Pseudo-random number with Gaussian distribution
virtual cvm::real rand_gaussian(void);
/// Pass restraint energy value for current timestep to MD engine
virtual void add_energy(cvm::real energy);
/// \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) const;
/// Recompute PBC reciprocal lattice (assumes XYZ periodicity)
void update_pbc_lattice();
/// Set the lattice vectors to zero
void reset_pbc_lattice();
/// \brief Tell the proxy whether total forces are needed (they may not
/// always be available)
virtual void request_total_force(bool yesno);
/// Are total forces being used?
virtual bool total_forces_enabled() const;
/// Are total forces from the current step available?
virtual bool total_forces_same_step() const;
/// Get the molecule ID when called in VMD; raise error otherwise
/// \param molid Set this argument equal to the current VMD molid
virtual int get_molid(int &molid);
/// Get value of alchemical lambda parameter from back-end (if available)
virtual int get_alch_lambda(cvm::real* lambda);
/// Set value of alchemical lambda parameter to be sent to back-end at end of timestep
void set_alch_lambda(cvm::real lambda);
/// Send cached value of alchemical lambda parameter to back-end (if available)
virtual int send_alch_lambda();
/// Get energy derivative with respect to lambda (if available)
virtual int get_dE_dlambda(cvm::real* dE_dlambda);
/// Apply a scalar force on dE_dlambda (back-end distributes it onto atoms)
virtual int apply_force_dE_dlambda(cvm::real* force);
/// Get energy second derivative with respect to lambda (if available)
virtual int get_d2E_dlambda2(cvm::real* d2E_dlambda2);
/// Force to be applied onto alch. lambda, propagated from biasing forces on dE_dlambda
cvm::real indirect_lambda_biasing_force;
/// Get weight factor from accelMD
virtual cvm::real get_accelMD_factor() const {
cvm::error("Error: accessing the reweighting factor of accelerated MD "
"is not yet implemented in the MD engine.\n",
COLVARS_NOT_IMPLEMENTED);
return 1.0;
}
virtual bool accelMD_enabled() const {
return false;
}
protected:
/// Next value of lambda to be sent to back-end
cvm::real cached_alch_lambda;
/// Whether lambda has been set and needs to be updated in backend
bool cached_alch_lambda_changed;
/// Whether the total forces have been requested
bool total_force_requested;
/// \brief Type of boundary conditions
///
/// Orthogonal and triclinic cells are made available to objects.
/// For any other conditions (mixed periodicity, triclinic cells in LAMMPS)
/// minimum-image distances are computed by the host engine regardless.
enum Boundaries_type {
boundaries_non_periodic,
boundaries_pbc_ortho,
boundaries_pbc_triclinic,
boundaries_unsupported
};
/// Type of boundary conditions
Boundaries_type boundaries_type;
/// Bravais lattice vectors
cvm::rvector unit_cell_x, unit_cell_y, unit_cell_z;
/// Reciprocal lattice vectors
cvm::rvector reciprocal_cell_x, reciprocal_cell_y, reciprocal_cell_z;
};
/// \brief Container of atomic data for processing by Colvars
class colvarproxy_atoms {
@ -229,7 +69,7 @@ public:
std::string const &segment_id);
/// \brief Used by the atom class destructor: rather than deleting the array slot
/// (costly) set the corresponding atoms_ncopies to zero
/// (costly) set the corresponding atoms_refcount to zero
virtual void clear_atom(int index);
/// \brief Select atom IDs from a file (usually PDB) \param filename name of
@ -260,37 +100,51 @@ public:
/// Clear atomic data
int reset();
/// Get the numeric ID of the given atom (for the program)
/// Get the numeric ID of the given atom
/// \param index Internal index in the Colvars arrays
inline int get_atom_id(int index) const
{
return atoms_ids[index];
}
/// Get the mass of the given atom
/// \param index Internal index in the Colvars arrays
inline cvm::real get_atom_mass(int index) const
{
return atoms_masses[index];
}
/// Increase the reference count of the given atom
/// \param index Internal index in the Colvars arrays
inline void increase_refcount(int index)
{
atoms_refcount[index] += 1;
}
/// Get the charge of the given atom
/// \param index Internal index in the Colvars arrays
inline cvm::real get_atom_charge(int index) const
{
return atoms_charges[index];
}
/// Read the current position of the given atom
/// \param index Internal index in the Colvars arrays
inline cvm::rvector get_atom_position(int index) const
{
return atoms_positions[index];
}
/// Read the current total force of the given atom
/// \param index Internal index in the Colvars arrays
inline cvm::rvector get_atom_total_force(int index) const
{
return atoms_total_forces[index];
}
/// Request that this force is applied to the given atom
/// \param index Internal index in the Colvars arrays
/// \param new_force Force to add
inline void apply_atom_force(int index, cvm::rvector const &new_force)
{
atoms_new_colvar_forces[index] += new_force;
@ -310,6 +164,9 @@ public:
return &atoms_ids;
}
/// Return number of atoms with positive reference count
size_t get_num_active_atoms() const;
inline std::vector<cvm::real> const *get_atom_masses() const
{
return &atoms_masses;
@ -406,7 +263,7 @@ protected:
/// within the host program
std::vector<int> atoms_ids;
/// \brief Keep track of how many times each atom is used by a separate colvar object
std::vector<size_t> atoms_ncopies;
std::vector<size_t> atoms_refcount;
/// \brief Masses of the atoms (allow redefinition during a run, as done e.g. in LAMMPS)
std::vector<cvm::real> atoms_masses;
/// \brief Charges of the atoms (allow redefinition during a run, as done e.g. in LAMMPS)
@ -510,6 +367,9 @@ public:
return &atom_groups_ids;
}
/// Return number of atom groups with positive reference count
size_t get_num_active_atom_groups() const;
inline std::vector<cvm::real> *modify_atom_group_masses()
{
// TODO updated_masses
@ -561,7 +421,7 @@ protected:
/// within the host program
std::vector<int> atom_groups_ids;
/// \brief Keep track of how many times each group is used by a separate cvc
std::vector<size_t> atom_groups_ncopies;
std::vector<size_t> atom_groups_refcount;
/// \brief Total masses of the atom groups
std::vector<cvm::real> atom_groups_masses;
/// \brief Total charges of the atom groups (allow redefinition during a run, as done e.g. in LAMMPS)
@ -584,6 +444,12 @@ protected:
};
#if defined(_OPENMP)
#include <omp.h>
#else
struct omp_lock_t;
#endif
/// \brief Methods for SMP parallelization
class colvarproxy_smp {
@ -629,7 +495,7 @@ public:
protected:
/// Lock state for OpenMP
void *omp_lock_state;
omp_lock_t *omp_lock_state;
};
@ -698,108 +564,6 @@ public:
};
/// Methods for data input/output
class colvarproxy_io {
public:
/// Constructor
colvarproxy_io();
/// Destructor
virtual ~colvarproxy_io();
/// \brief Save the current frame number in the argument given
// Returns error code
virtual int get_frame(long int &);
/// \brief Set the current frame number (as well as colvarmodule::it)
// Returns error code
virtual int set_frame(long int);
/// \brief Rename the given file, before overwriting it
virtual int backup_file(char const *filename);
/// \brief Rename the given file, before overwriting it
inline int backup_file(std::string const &filename)
{
return backup_file(filename.c_str());
}
/// Remove the given file (on Windows only, rename to filename.old)
virtual int remove_file(char const *filename);
/// Remove the given file (on Windows only, rename to filename.old)
inline int remove_file(std::string const &filename)
{
return remove_file(filename.c_str());
}
/// Rename the given file
virtual int rename_file(char const *filename, char const *newfilename);
/// Rename the given file
inline int rename_file(std::string const &filename,
std::string const &newfilename)
{
return rename_file(filename.c_str(), newfilename.c_str());
}
/// Prefix of the input state file to be read next
inline std::string & input_prefix()
{
return input_prefix_str;
}
/// Default prefix to be used for all output files (final configuration)
inline std::string & output_prefix()
{
return output_prefix_str;
}
/// Prefix of the restart (checkpoint) file to be written next
inline std::string & restart_output_prefix()
{
return restart_output_prefix_str;
}
/// Default restart frequency (as set by the simulation engine)
inline int default_restart_frequency() const
{
return restart_frequency_engine;
}
/// Buffer from which the input state information may be read
inline char const * & input_buffer()
{
return input_buffer_;
}
protected:
/// Prefix of the input state file to be read next
std::string input_prefix_str;
/// Default prefix to be used for all output files (final configuration)
std::string output_prefix_str;
/// Prefix of the restart (checkpoint) file to be written next
std::string restart_output_prefix_str;
/// How often the simulation engine will write its own restart
int restart_frequency_engine;
/// \brief Currently opened output files: by default, these are ofstream objects.
/// Allows redefinition to implement different output mechanisms
std::list<std::ostream *> output_files;
/// \brief Identifiers for output_stream objects: by default, these are the names of the files
std::list<std::string> output_stream_names;
/// Buffer from which the input state information may be read
char const *input_buffer_;
};
/// \brief Interface between the collective variables module and
/// the simulation or analysis program (NAMD, VMD, LAMMPS...).
@ -827,6 +591,8 @@ public:
/// Destructor
virtual ~colvarproxy();
virtual bool io_available() /* override */;
/// Request deallocation of the module (currently only implemented by VMD)
virtual int request_deletion();
@ -839,21 +605,30 @@ public:
/// \brief Reset proxy state, e.g. requested atoms
virtual int reset();
/// Close any open files to prevent data loss
int close_files();
/// (Re)initialize the module
virtual int parse_module_config();
/// (Re)initialize required member data after construction
/// (Re)initialize required member data (called after the module)
virtual int setup();
/// \brief Update data required by the colvars module (e.g. cache atom positions)
/// Whether the engine allows to fully initialize Colvars immediately
inline bool engine_ready() const
{
return engine_ready_;
}
/// Enqueue new configuration text, to be parsed as soon as possible
void add_config(std::string const &cmd, std::string const &conf);
/// Update data required by Colvars module (e.g. read atom positions)
///
/// TODO Break up colvarproxy_namd and colvarproxy_lammps function into these
virtual int update_input();
/// \brief Update data based from the results of a module update (e.g. send forces)
/// Update data based on the results of a Colvars call (e.g. send forces)
virtual int update_output();
/// Carry out operations needed before next step is run
/// Carry out operations needed before next simulation step is run
int end_of_step();
/// Print a message to the main log
@ -903,26 +678,11 @@ public:
return version_int;
}
/// \brief Returns a reference to the given output channel;
/// if this is not open already, then open it
virtual std::ostream *output_stream(std::string const &output_name,
std::ios_base::openmode mode =
std::ios_base::out);
/// Returns a reference to output_name if it exists, NULL otherwise
virtual std::ostream *get_output_stream(std::string const &output_name);
/// \brief Flushes the given output channel
virtual int flush_output_stream(std::ostream *os);
/// \brief Flushes all output channels
virtual int flush_output_streams();
/// \brief Closes the given output channel
virtual int close_output_stream(std::string const &output_name);
protected:
/// Whether the engine allows to fully initialize Colvars immediately
bool engine_ready_;
/// Collected error messages
std::string error_output;
@ -943,8 +703,10 @@ protected:
/// Track which features have been acknowledged during the last run
size_t features_hash;
/// Raise when the output stream functions are used on threads other than 0
void smp_stream_error();
private:
/// Queue of config strings or files to be fed to the module
void *config_queue_;
};

310
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@ -0,0 +1,310 @@
// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
// Using access() to check if a file exists (until we can assume C++14/17)
#if !defined(_WIN32) || defined(__CYGWIN__)
#include <unistd.h>
#endif
#if defined(_WIN32)
#include <io.h>
#endif
#include <cerrno>
#include <cstdio>
#include <list>
#include <map>
#include <sstream>
#include <fstream>
#include "colvarmodule.h"
#include "colvarproxy_io.h"
colvarproxy_io::colvarproxy_io()
{
input_buffer_ = NULL;
restart_frequency_engine = 0;
input_stream_error_ = new std::istringstream();
input_stream_error_->setstate(std::ios::badbit);
output_stream_error_ = new std::ostringstream();
output_stream_error_->setstate(std::ios::badbit);
}
colvarproxy_io::~colvarproxy_io()
{
delete input_stream_error_;
close_input_streams();
delete output_stream_error_;
close_output_streams();
}
bool colvarproxy_io::io_available()
{
return false;
}
int colvarproxy_io::get_frame(long int&)
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_io::set_frame(long int)
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_io::backup_file(char const *filename)
{
// Simplified version of NAMD_file_exists()
int exit_code;
do {
#if defined(_WIN32) && !defined(__CYGWIN__)
// We could use _access_s here, but it is probably too new
exit_code = _access(filename, 00);
#else
exit_code = access(filename, F_OK);
#endif
} while ((exit_code != 0) && (errno == EINTR));
if (exit_code != 0) {
if (errno == ENOENT) {
// File does not exist
return COLVARS_OK;
} else {
return cvm::error("Unknown error while checking if file \""+
std::string(filename)+"\" exists.\n", COLVARS_ERROR);
}
}
// The file exists, then rename it
if (std::string(filename).rfind(std::string(".colvars.state")) !=
std::string::npos) {
return rename_file(filename, (std::string(filename)+".old").c_str());
} else {
return rename_file(filename, (std::string(filename)+".BAK").c_str());
}
}
int colvarproxy_io::remove_file(char const *filename)
{
int error_code = COLVARS_OK;
#if defined(_WIN32) && !defined(__CYGWIN__)
// Because the file may be open by other processes, rename it to filename.old
std::string const renamed_file(std::string(filename)+".old");
// It may still be there from an interrupted run, so remove it to be safe
std::remove(renamed_file.c_str());
int rename_exit_code = 0;
while ((rename_exit_code = std::rename(filename,
renamed_file.c_str())) != 0) {
if (errno == EINTR) continue;
error_code |= COLVARS_FILE_ERROR;
break;
}
// Ask to remove filename.old, but ignore any errors raised
std::remove(renamed_file.c_str());
#else
if (std::remove(filename)) {
if (errno != ENOENT) {
error_code |= COLVARS_FILE_ERROR;
}
}
#endif
if (error_code != COLVARS_OK) {
return cvm::error("Error: in removing file \""+std::string(filename)+
"\".\n.",
error_code);
}
return COLVARS_OK;
}
int colvarproxy_io::rename_file(char const *filename, char const *newfilename)
{
int error_code = COLVARS_OK;
#if defined(_WIN32) && !defined(__CYGWIN__)
// On straight Windows, must remove the destination before renaming it
error_code |= remove_file(newfilename);
#endif
int rename_exit_code = 0;
while ((rename_exit_code = std::rename(filename, newfilename)) != 0) {
if (errno == EINTR) continue;
// Call log() instead of error to allow the next try
cvm::log("Error: in renaming file \""+std::string(filename)+"\" to \""+
std::string(newfilename)+"\".\n.");
error_code |= COLVARS_FILE_ERROR;
if (errno == EXDEV) continue;
break;
}
return rename_exit_code ? error_code : COLVARS_OK;
}
std::istream &colvarproxy_io::input_stream(std::string const &input_name,
std::string const description,
bool error_on_fail)
{
if (!io_available()) {
cvm::error("Error: trying to access an input file/channel "
"from the wrong thread.\n", COLVARS_BUG_ERROR);
return *input_stream_error_;
}
if (colvarproxy_io::input_stream_exists(input_name)) {
return *(input_streams_[input_name]);
}
// Using binary to work around differences in line termination conventions
// See https://github.com/Colvars/colvars/commit/8236879f7de4
input_streams_[input_name] = new std::ifstream(input_name.c_str(),
std::ios::binary);
if (input_streams_[input_name]->fail() && error_on_fail) {
cvm::error("Error: cannot open "+description+" \""+input_name+"\".\n",
COLVARS_FILE_ERROR);
}
return *(input_streams_[input_name]);
}
bool colvarproxy_io::input_stream_exists(std::string const &input_name)
{
return (input_streams_.count(input_name) > 0);
}
int colvarproxy_io::close_input_stream(std::string const &input_name)
{
if (colvarproxy_io::input_stream_exists(input_name)) {
delete input_streams_[input_name];
input_streams_.erase(input_name);
return COLVARS_OK;
}
return cvm::error("Error: input file/channel \""+input_name+
"\" does not exist.\n", COLVARS_FILE_ERROR);
}
int colvarproxy_io::close_input_streams()
{
for (std::map<std::string, std::istream *>::iterator ii = input_streams_.begin();
ii != input_streams_.end();
ii++) {
delete ii->second;
}
input_streams_.clear();
return COLVARS_OK;
}
std::ostream & colvarproxy_io::output_stream(std::string const &output_name,
std::string const description)
{
if (cvm::debug()) {
cvm::log("Using colvarproxy_io::output_stream()\n");
}
if (!io_available()) {
cvm::error("Error: trying to access an output file/channel "
"from the wrong thread.\n", COLVARS_BUG_ERROR);
return *output_stream_error_;
}
if (colvarproxy_io::output_stream_exists(output_name)) {
return *(output_streams_[output_name]);
}
backup_file(output_name.c_str());
output_streams_[output_name] = new std::ofstream(output_name.c_str());
if (!*(output_streams_[output_name])) {
cvm::error("Error: cannot write to "+description+" \""+output_name+"\".\n",
COLVARS_FILE_ERROR);
}
return *(output_streams_[output_name]);
}
bool colvarproxy_io::output_stream_exists(std::string const &output_name)
{
return (output_streams_.count(output_name) > 0);
}
int colvarproxy_io::flush_output_stream(std::string const &output_name)
{
if (!io_available()) {
// No-op
return COLVARS_OK;
}
if (colvarproxy_io::output_stream_exists(output_name)) {
(dynamic_cast<std::ofstream *>(output_streams_[output_name]))->flush();
return COLVARS_OK;
}
return COLVARS_OK;
}
int colvarproxy_io::flush_output_streams()
{
if (!io_available()) {
return COLVARS_OK;
}
for (std::map<std::string, std::ostream *>::iterator osi = output_streams_.begin();
osi != output_streams_.end();
osi++) {
(dynamic_cast<std::ofstream *>(osi->second))->flush();
}
return COLVARS_OK;
}
int colvarproxy_io::close_output_stream(std::string const &output_name)
{
if (!io_available()) {
return cvm::error("Error: trying to access an output file/channel "
"from the wrong thread.\n", COLVARS_BUG_ERROR);
}
if (colvarproxy_io::output_stream_exists(output_name)) {
(dynamic_cast<std::ofstream *>(output_streams_[output_name]))->close();
delete output_streams_[output_name];
output_streams_.erase(output_name);
}
return COLVARS_OK;
}
int colvarproxy_io::close_output_streams()
{
if (! io_available()) {
return COLVARS_OK;
}
for (std::map<std::string, std::ostream *>::iterator osi = output_streams_.begin();
osi != output_streams_.end();
osi++) {
(dynamic_cast<std::ofstream *>(osi->second))->close();
}
output_streams_.clear();
return COLVARS_OK;
}

167
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@ -0,0 +1,167 @@
// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#ifndef COLVARPROXY_IO_H
#define COLVARPROXY_IO_H
#include <map>
#include <string>
#include <iosfwd>
/// Methods for data input/output
class colvarproxy_io {
public:
/// Constructor
colvarproxy_io();
/// Destructor
virtual ~colvarproxy_io();
/// Ensure that we're on the main thread (derived class will do actual check)
virtual bool io_available();
/// \brief Save the current frame number in the argument given
// Returns error code
virtual int get_frame(long int &);
/// \brief Set the current frame number (as well as colvarmodule::it)
// Returns error code
virtual int set_frame(long int);
/// \brief Rename the given file, before overwriting it
virtual int backup_file(char const *filename);
/// \brief Rename the given file, before overwriting it
inline int backup_file(std::string const &filename)
{
return backup_file(filename.c_str());
}
/// Remove the given file (on Windows only, rename to filename.old)
virtual int remove_file(char const *filename);
/// Remove the given file (on Windows only, rename to filename.old)
inline int remove_file(std::string const &filename)
{
return remove_file(filename.c_str());
}
/// Rename the given file
virtual int rename_file(char const *filename, char const *newfilename);
/// Rename the given file
inline int rename_file(std::string const &filename,
std::string const &newfilename)
{
return rename_file(filename.c_str(), newfilename.c_str());
}
/// Prefix of the input state file to be read next
inline std::string & input_prefix()
{
return input_prefix_str;
}
/// Default prefix to be used for all output files (final configuration)
inline std::string & output_prefix()
{
return output_prefix_str;
}
/// Prefix of the restart (checkpoint) file to be written next
inline std::string & restart_output_prefix()
{
return restart_output_prefix_str;
}
/// Default restart frequency (as set by the simulation engine)
inline int default_restart_frequency() const
{
return restart_frequency_engine;
}
/// Buffer from which the input state information may be read
inline char const * & input_buffer()
{
return input_buffer_;
}
/// Returns a reference to given input stream, creating it if needed
/// \param input_name File name (later only a handle)
/// \param description Purpose of the file
/// \param error_on_fail Raise error when failing to open (allow testing)
virtual std::istream &input_stream(std::string const &input_name,
std::string const description = "file/channel",
bool error_on_fail = true);
/// Check if the file/channel is open (without opening it if not)
virtual bool input_stream_exists(std::string const &input_name);
/// Closes the given input stream
virtual int close_input_stream(std::string const &input_name);
/// Closes all input streams
virtual int close_input_streams();
/// Returns a reference to the named output file/channel (open it if needed)
/// \param output_name File name or identifier
/// \param description Purpose of the file
virtual std::ostream &output_stream(std::string const &output_name,
std::string const description = "file/channel");
/// Check if the file/channel is open (without opening it if not)
virtual bool output_stream_exists(std::string const &output_name);
/// Flushes the given output file/channel
virtual int flush_output_stream(std::string const &output_name);
/// Flushes all output files/channels
virtual int flush_output_streams();
/// Closes the given output file/channel
virtual int close_output_stream(std::string const &output_name);
/// Close all open files/channels to prevent data loss
virtual int close_output_streams();
protected:
/// Prefix of the input state file to be read next
std::string input_prefix_str;
/// Default prefix to be used for all output files (final configuration)
std::string output_prefix_str;
/// Prefix of the restart (checkpoint) file to be written next
std::string restart_output_prefix_str;
/// How often the simulation engine will write its own restart
int restart_frequency_engine;
/// Container of input files/channels indexed by path name
std::map<std::string, std::istream *> input_streams_;
/// Object whose reference is returned when read errors occur
std::istream *input_stream_error_;
/// Currently open output files/channels
std::map<std::string, std::ostream *> output_streams_;
/// Object whose reference is returned when write errors occur
std::ostream *output_stream_error_;
/// Buffer from which the input state information may be read
char const *input_buffer_;
};
#endif

203
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@ -0,0 +1,203 @@
// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include "colvarmodule.h"
#include "colvartypes.h"
#include "colvarproxy_system.h"
colvarproxy_system::colvarproxy_system()
{
angstrom_value_ = 0.0;
kcal_mol_value_ = 0.0;
target_temperature_ = 0.0;
boltzmann_ = 0.001987191; // Default: kcal/mol/K
boundaries_type = boundaries_unsupported;
total_force_requested = false;
indirect_lambda_biasing_force = 0.0;
cached_alch_lambda_changed = false;
cached_alch_lambda = -1.0;
reset_pbc_lattice();
}
colvarproxy_system::~colvarproxy_system() {}
int colvarproxy_system::set_unit_system(std::string const & /* units */,
bool /* check_only */)
{
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_system::set_target_temperature(cvm::real T)
{
target_temperature_ = T;
return COLVARS_OK;
}
cvm::real colvarproxy_system::dt()
{
// TODO define, document and implement a user method to set the value of this
return 1.0;
}
cvm::real colvarproxy_system::rand_gaussian()
{
// TODO define, document and implement a user method to set the value of this
return 0.0;
}
void colvarproxy_system::add_energy(cvm::real /* energy */) {}
void colvarproxy_system::request_total_force(bool yesno)
{
if (yesno == true)
cvm::error("Error: total forces are currently not implemented.\n",
COLVARS_NOT_IMPLEMENTED);
}
bool colvarproxy_system::total_forces_enabled() const
{
return false;
}
bool colvarproxy_system::total_forces_same_step() const
{
return false;
}
inline int round_to_integer(cvm::real x)
{
return int(cvm::floor(x+0.5));
}
void colvarproxy_system::update_pbc_lattice()
{
// Periodicity is assumed in all directions
if (boundaries_type == boundaries_unsupported ||
boundaries_type == boundaries_non_periodic) {
cvm::error("Error: setting PBC lattice with unsupported boundaries.\n",
COLVARS_BUG_ERROR);
return;
}
{
cvm::rvector const v = cvm::rvector::outer(unit_cell_y, unit_cell_z);
reciprocal_cell_x = v/(v*unit_cell_x);
}
{
cvm::rvector const v = cvm::rvector::outer(unit_cell_z, unit_cell_x);
reciprocal_cell_y = v/(v*unit_cell_y);
}
{
cvm::rvector const v = cvm::rvector::outer(unit_cell_x, unit_cell_y);
reciprocal_cell_z = v/(v*unit_cell_z);
}
}
void colvarproxy_system::reset_pbc_lattice()
{
unit_cell_x.reset();
unit_cell_y.reset();
unit_cell_z.reset();
reciprocal_cell_x.reset();
reciprocal_cell_y.reset();
reciprocal_cell_z.reset();
}
cvm::rvector colvarproxy_system::position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
const
{
if (boundaries_type == boundaries_unsupported) {
cvm::error("Error: unsupported boundary conditions.\n", COLVARS_INPUT_ERROR);
}
cvm::rvector diff = (pos2 - pos1);
if (boundaries_type == boundaries_non_periodic) return diff;
cvm::real const x_shift = round_to_integer(reciprocal_cell_x*diff);
cvm::real const y_shift = round_to_integer(reciprocal_cell_y*diff);
cvm::real const z_shift = round_to_integer(reciprocal_cell_z*diff);
diff.x -= x_shift*unit_cell_x.x + y_shift*unit_cell_y.x +
z_shift*unit_cell_z.x;
diff.y -= x_shift*unit_cell_x.y + y_shift*unit_cell_y.y +
z_shift*unit_cell_z.y;
diff.z -= x_shift*unit_cell_x.z + y_shift*unit_cell_y.z +
z_shift*unit_cell_z.z;
return diff;
}
int colvarproxy_system::get_molid(int &)
{
cvm::error("Error: only VMD allows the use of multiple \"molecules\", "
"i.e. multiple molecular systems.", COLVARS_NOT_IMPLEMENTED);
return -1;
}
int colvarproxy_system::get_alch_lambda(cvm::real * /* lambda */)
{
return cvm::error("Error in get_alch_lambda: alchemical lambda dynamics is not supported by this build.",
COLVARS_NOT_IMPLEMENTED);
}
void colvarproxy_system::set_alch_lambda(cvm::real lambda)
{
cached_alch_lambda = lambda;
cached_alch_lambda_changed = true;
}
int colvarproxy_system::send_alch_lambda()
{
return cvm::error("Error in set_alch_lambda: alchemical lambda dynamics is not supported by this build.",
COLVARS_NOT_IMPLEMENTED);
}
int colvarproxy_system::get_dE_dlambda(cvm::real * /* force */)
{
return cvm::error("Error in get_dE_dlambda: alchemical lambda dynamics is not supported by this build.",
COLVARS_NOT_IMPLEMENTED);
}
int colvarproxy_system::apply_force_dE_dlambda(cvm::real* /* force */)
{
return cvm::error("Error in apply_force_dE_dlambda: function is not implemented by this build.",
COLVARS_NOT_IMPLEMENTED);
}
int colvarproxy_system::get_d2E_dlambda2(cvm::real*)
{
return cvm::error("Error in get_d2E_dlambda2: function is not implemented by this build.",
COLVARS_NOT_IMPLEMENTED);
}

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@ -0,0 +1,177 @@
// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#ifndef COLVARPROXY_SYSTEM_H
#define COLVARPROXY_SYSTEM_H
/// Methods for accessing the simulation system (PBCs, integrator, etc)
class colvarproxy_system {
public:
/// Constructor
colvarproxy_system();
/// Destructor
virtual ~colvarproxy_system();
/// \brief Name of the unit system used internally by Colvars (by default, that of the back-end).
/// Supported depending on the back-end: real (A, kcal/mol), metal (A, eV), electron (Bohr, Hartree), gromacs (nm, kJ/mol)
/// Note: calls to back-end PBC functions assume back-end length unit
/// We use different unit from back-end in VMD bc using PBC functions from colvarproxy base class
/// Colvars internal units are user specified, because the module exchanges info in unknown
/// composite dimensions with user input, while it only exchanges quantities of known
/// dimension with the back-end (length and forces)
std::string units;
/// \brief Request to set the units used internally by Colvars
virtual int set_unit_system(std::string const &units, bool check_only);
/// \brief Convert a length from Angstrom to internal
inline cvm::real angstrom_to_internal(cvm::real l) const
{
return l * angstrom_value_;
}
/// \brief Convert a length from internal to Angstrom
inline cvm::real internal_to_angstrom(cvm::real l) const
{
return l / angstrom_value_;
}
/// Boltzmann constant, with unit the same as energy / K
inline cvm::real boltzmann() const
{
return boltzmann_;
}
/// Current target temperature of the simulation (K units)
inline cvm::real target_temperature() const
{
return target_temperature_;
}
/// Set the current target temperature of the simulation (K units)
virtual int set_target_temperature(cvm::real T);
/// \brief Time step of the simulation (fs)
virtual cvm::real dt();
/// \brief Pseudo-random number with Gaussian distribution
virtual cvm::real rand_gaussian(void);
/// Pass restraint energy value for current timestep to MD engine
virtual void add_energy(cvm::real energy);
/// \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) const;
/// Recompute PBC reciprocal lattice (assumes XYZ periodicity)
void update_pbc_lattice();
/// Set the lattice vectors to zero
void reset_pbc_lattice();
/// \brief Tell the proxy whether total forces are needed (they may not
/// always be available)
virtual void request_total_force(bool yesno);
/// Are total forces being used?
virtual bool total_forces_enabled() const;
/// Are total forces from the current step available?
virtual bool total_forces_same_step() const;
/// Get the molecule ID when called in VMD; raise error otherwise
/// \param molid Set this argument equal to the current VMD molid
virtual int get_molid(int &molid);
/// Get value of alchemical lambda parameter from back-end (if available)
virtual int get_alch_lambda(cvm::real* lambda);
/// Set value of alchemical lambda parameter to be sent to back-end at end of timestep
void set_alch_lambda(cvm::real lambda);
/// Send cached value of alchemical lambda parameter to back-end (if available)
virtual int send_alch_lambda();
/// Get energy derivative with respect to lambda (if available)
virtual int get_dE_dlambda(cvm::real* dE_dlambda);
/// Apply a scalar force on dE_dlambda (back-end distributes it onto atoms)
virtual int apply_force_dE_dlambda(cvm::real* force);
/// Get energy second derivative with respect to lambda (if available)
virtual int get_d2E_dlambda2(cvm::real* d2E_dlambda2);
/// Force to be applied onto alch. lambda, propagated from biasing forces on dE_dlambda
cvm::real indirect_lambda_biasing_force;
/// Get weight factor from accelMD
virtual cvm::real get_accelMD_factor() const {
cvm::error("Error: accessing the reweighting factor of accelerated MD "
"is not yet implemented in the MD engine.\n",
COLVARS_NOT_IMPLEMENTED);
return 1.0;
}
virtual bool accelMD_enabled() const {
return false;
}
protected:
/// Next value of lambda to be sent to back-end
cvm::real cached_alch_lambda;
/// Whether lambda has been set and needs to be updated in backend
bool cached_alch_lambda_changed;
/// Boltzmann constant in internal Colvars units
cvm::real boltzmann_;
/// Most up to date target temperature for the system (in K)
cvm::real target_temperature_;
/// \brief Value of 1 Angstrom in the internal (front-end) Colvars unit for atomic coordinates
/// * defaults to 0 in the base class; derived proxy classes must set it
/// * in VMD proxy, can only be changed when no variables are defined
/// as user-defined values in composite units must be compatible with that system
cvm::real angstrom_value_;
/// \brief Value of 1 kcal/mol in the internal Colvars unit for energy
cvm::real kcal_mol_value_;
/// Whether the total forces have been requested
bool total_force_requested;
/// \brief Type of boundary conditions
///
/// Orthogonal and triclinic cells are made available to objects.
/// For any other conditions (mixed periodicity, triclinic cells in LAMMPS)
/// minimum-image distances are computed by the host engine regardless.
enum Boundaries_type {
boundaries_non_periodic,
boundaries_pbc_ortho,
boundaries_pbc_triclinic,
boundaries_unsupported
};
/// Type of boundary conditions
Boundaries_type boundaries_type;
/// Bravais lattice vectors
cvm::rvector unit_cell_x, unit_cell_y, unit_cell_z;
/// Reciprocal lattice vectors
cvm::rvector reciprocal_cell_x, reciprocal_cell_y, reciprocal_cell_z;
};
#endif

1
lib/colvars/colvarproxy_tcl.cpp
View File

@ -8,6 +8,7 @@
// Colvars repository at GitHub.
#include <sstream>
#include <iostream>
#include "colvarmodule.h"
#include "colvarproxy.h"

8
lib/colvars/colvarproxy_volmaps.cpp
View File

@ -33,7 +33,7 @@ int colvarproxy_volmaps::reset()
clear_volmap(i);
}
volmaps_ids.clear();
volmaps_ncopies.clear();
volmaps_refcount.clear();
volmaps_values.clear();
volmaps_new_colvar_forces.clear();
return COLVARS_OK;
@ -43,7 +43,7 @@ int colvarproxy_volmaps::reset()
int colvarproxy_volmaps::add_volmap_slot(int volmap_id)
{
volmaps_ids.push_back(volmap_id);
volmaps_ncopies.push_back(1);
volmaps_refcount.push_back(1);
volmaps_values.push_back(0.0);
volmaps_new_colvar_forces.push_back(0.0);
return (volmaps_ids.size() - 1);
@ -95,8 +95,8 @@ void colvarproxy_volmaps::clear_volmap(int index)
"previously requested.\n", COLVARS_INPUT_ERROR);
}
if (volmaps_ncopies[index] > 0) {
volmaps_ncopies[index] -= 1;
if (volmaps_refcount[index] > 0) {
volmaps_refcount[index] -= 1;
}
}

2
lib/colvars/colvarproxy_volmaps.h
View File

@ -108,7 +108,7 @@ protected:
/// \brief Keep track of how many times each vol map is used by a
/// separate colvar object
std::vector<size_t> volmaps_ncopies;
std::vector<size_t> volmaps_refcount;
/// \brief Current values of the vol maps
std::vector<cvm::real> volmaps_values;

2
lib/colvars/colvars_version.h
View File

@ -1,3 +1,3 @@
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2022-05-24"
#define COLVARS_VERSION "2023-05-01"
#endif

81
lib/colvars/colvarscript_commands.h
View File

@ -134,11 +134,19 @@ CVSCRIPT(cv_config,
char const *conf_str =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
std::string const conf(conf_str);
if (cvm::main()->read_config_string(conf) == COLVARS_OK) {
script->proxy()->add_config("config", conf);
if (script->proxy()->engine_ready()) {
// Engine allows immediate initialization
if ((script->proxy()->parse_module_config() |
script->proxy()->setup()) == COLVARS_OK) {
return COLVARS_OK;
}
} else {
script->add_error_msg("Error parsing configuration string");
return COLVARSCRIPT_ERROR;
}
}
// Engine not ready, config will be read during proxy->setup()
return COLVARS_OK;
)
CVSCRIPT(cv_configfile,
@ -147,12 +155,19 @@ CVSCRIPT(cv_configfile,
"conf_file : string - Path to configuration file",
char const *conf_file_name =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
if (script->module()->read_config_file(conf_file_name) == COLVARS_OK) {
script->proxy()->add_config("configfile", std::string(conf_file_name));
if (script->proxy()->engine_ready()) {
// Engine allows immediate initialization
if ((script->proxy()->parse_module_config() |
script->proxy()->setup()) == COLVARS_OK) {
return COLVARS_OK;
} else {
script->add_error_msg("Error parsing configuration file");
return COLVARSCRIPT_ERROR;
}
}
// Engine not ready, config will be read during proxy->setup()
return COLVARS_OK;
)
CVSCRIPT(cv_delete,
@ -309,6 +324,51 @@ CVSCRIPT(cv_getenergy,
return COLVARS_OK;
)
CVSCRIPT(cv_getnumactiveatomgroups,
"Get the number of atom groups that currently have positive ref counts\n"
"count : integer - Total number of atom groups",
0, 0,
"",
script->set_result_int(static_cast<int>(script->proxy()->get_num_active_atom_groups()));
return COLVARS_OK;
)
CVSCRIPT(cv_getnumactiveatoms,
"Get the number of atoms that currently have positive ref counts\n"
"count : integer - Total number of atoms",
0, 0,
"",
script->set_result_int(static_cast<int>(script->proxy()->get_num_active_atoms()));
return COLVARS_OK;
)
CVSCRIPT(cv_getnumatoms,
"Get the number of requested atoms, including those not in use now\n"
"count : integer - Total number of atoms",
0, 0,
"",
script->set_result_int(static_cast<int>(script->proxy()->get_atom_ids()->size()));
return COLVARS_OK;
)
CVSCRIPT(cv_getstepabsolute,
"Get the current step number of the simulation (including restarts)\n"
"step : int - Absolute step number",
0, 0,
"",
script->set_result_int(cvm::step_absolute());
return COLVARS_OK;
)
CVSCRIPT(cv_getsteprelative,
"Get the current step number from the start of this job\n"
"step : int - Relative step number",
0, 0,
"",
script->set_result_int(cvm::step_relative());
return COLVARS_OK;
)
CVSCRIPT(cv_help,
"Get the help string of the Colvars scripting interface\n"
"help : string - Help string",
@ -481,6 +541,7 @@ CVSCRIPT(cv_reset,
"Delete all internal configuration",
0, 0,
"",
cvm::log("Resetting the Collective Variables module.");
return script->module()->reset();
)
@ -516,6 +577,20 @@ CVSCRIPT(cv_savetostring,
return script->module()->write_restart_string(script->modify_str_result());
)
CVSCRIPT(cv_targettemperature,
"Get/set target temperature, overriding what the MD engine provides\n"
"T : float - Current target temperature in K",
0, 1,
"T : float - New target temperature in K",
char const *Targ =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
if (Targ == NULL) {
return script->set_result_real(script->proxy()->target_temperature());
} else {
return script->proxy()->set_target_temperature(strtod(Targ, NULL));
}
)
CVSCRIPT(cv_units,
"Get or set the current Colvars unit system\n"
"units : string - The current unit system",

69
lib/colvars/colvartypes.cpp
View File

@ -125,33 +125,6 @@ std::ostream & operator << (std::ostream &os, colvarmodule::quaternion const &q)
std::istream & operator >> (std::istream &is, colvarmodule::quaternion &q)
{
std::streampos const start_pos = is.tellg();
std::string euler("");
if ( (is >> euler) && (colvarparse::to_lower_cppstr(euler) ==
std::string("euler")) ) {
// parse the Euler angles
char sep;
cvm::real phi, theta, psi;
if ( !(is >> sep) || !(sep == '(') ||
!(is >> phi) || !(is >> sep) || !(sep == ',') ||
!(is >> theta) || !(is >> sep) || !(sep == ',') ||
!(is >> psi) || !(is >> sep) || !(sep == ')') ) {
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
q = colvarmodule::quaternion(phi, theta, psi);
} else {
// parse the quaternion components
is.seekg(start_pos, std::ios::beg);
char sep;
if ( !(is >> sep) || !(sep == '(') ||
!(is >> q.q0) || !(is >> sep) || !(sep == ',') ||
@ -161,10 +134,7 @@ std::istream & operator >> (std::istream &is, colvarmodule::quaternion &q)
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
}
return is;
}
@ -318,15 +288,15 @@ void colvarmodule::rotation::build_correlation_matrix(
// build the correlation matrix
size_t i;
for (i = 0; i < pos1.size(); i++) {
C.xx() += pos1[i].x * pos2[i].x;
C.xy() += pos1[i].x * pos2[i].y;
C.xz() += pos1[i].x * pos2[i].z;
C.yx() += pos1[i].y * pos2[i].x;
C.yy() += pos1[i].y * pos2[i].y;
C.yz() += pos1[i].y * pos2[i].z;
C.zx() += pos1[i].z * pos2[i].x;
C.zy() += pos1[i].z * pos2[i].y;
C.zz() += pos1[i].z * pos2[i].z;
C.xx += pos1[i].x * pos2[i].x;
C.xy += pos1[i].x * pos2[i].y;
C.xz += pos1[i].x * pos2[i].z;
C.yx += pos1[i].y * pos2[i].x;
C.yy += pos1[i].y * pos2[i].y;
C.yz += pos1[i].y * pos2[i].z;
C.zx += pos1[i].z * pos2[i].x;
C.zy += pos1[i].z * pos2[i].y;
C.zz += pos1[i].z * pos2[i].z;
}
}
@ -335,22 +305,22 @@ void colvarmodule::rotation::compute_overlap_matrix()
{
// build the "overlap" matrix, whose eigenvectors are stationary
// points of the RMSD in the space of rotations
S[0][0] = C.xx() + C.yy() + C.zz();
S[1][0] = C.yz() - C.zy();
S[0][0] = C.xx + C.yy + C.zz;
S[1][0] = C.yz - C.zy;
S[0][1] = S[1][0];
S[2][0] = - C.xz() + C.zx() ;
S[2][0] = - C.xz + C.zx ;
S[0][2] = S[2][0];
S[3][0] = C.xy() - C.yx();
S[3][0] = C.xy - C.yx;
S[0][3] = S[3][0];
S[1][1] = C.xx() - C.yy() - C.zz();
S[2][1] = C.xy() + C.yx();
S[1][1] = C.xx - C.yy - C.zz;
S[2][1] = C.xy + C.yx;
S[1][2] = S[2][1];
S[3][1] = C.xz() + C.zx();
S[3][1] = C.xz + C.zx;
S[1][3] = S[3][1];
S[2][2] = - C.xx() + C.yy() - C.zz();
S[3][2] = C.yz() + C.zy();
S[2][2] = - C.xx + C.yy - C.zz;
S[3][2] = C.yz + C.zy;
S[2][3] = S[3][2];
S[3][3] = - C.xx() - C.yy() + C.zz();
S[3][3] = - C.xx - C.yy + C.zz;
}
@ -402,7 +372,6 @@ void colvarmodule::rotation::calc_optimal_rotation(
std::vector<cvm::atom_pos> const &pos1,
std::vector<cvm::atom_pos> const &pos2)
{
C.resize(3, 3);
C.reset();
build_correlation_matrix(pos1, pos2);

128
lib/colvars/colvartypes.h
View File

@ -868,105 +868,67 @@ public:
/// \brief 2-dimensional array of real numbers with three components
/// along each dimension (works with colvarmodule::rvector)
class colvarmodule::rmatrix
: public colvarmodule::matrix2d<colvarmodule::real> {
private:
class colvarmodule::rmatrix {
public:
/// Return the xx element
inline cvm::real & xx() { return (*this)[0][0]; }
/// Return the xy element
inline cvm::real & xy() { return (*this)[0][1]; }
/// Return the xz element
inline cvm::real & xz() { return (*this)[0][2]; }
/// Return the yx element
inline cvm::real & yx() { return (*this)[1][0]; }
/// Return the yy element
inline cvm::real & yy() { return (*this)[1][1]; }
/// Return the yz element
inline cvm::real & yz() { return (*this)[1][2]; }
/// Return the zx element
inline cvm::real & zx() { return (*this)[2][0]; }
/// Return the zy element
inline cvm::real & zy() { return (*this)[2][1]; }
/// Return the zz element
inline cvm::real & zz() { return (*this)[2][2]; }
/// Return the xx element
inline cvm::real xx() const { return (*this)[0][0]; }
/// Return the xy element
inline cvm::real xy() const { return (*this)[0][1]; }
/// Return the xz element
inline cvm::real xz() const { return (*this)[0][2]; }
/// Return the yx element
inline cvm::real yx() const { return (*this)[1][0]; }
/// Return the yy element
inline cvm::real yy() const { return (*this)[1][1]; }
/// Return the yz element
inline cvm::real yz() const { return (*this)[1][2]; }
/// Return the zx element
inline cvm::real zx() const { return (*this)[2][0]; }
/// Return the zy element
inline cvm::real zy() const { return (*this)[2][1]; }
/// Return the zz element
inline cvm::real zz() const { return (*this)[2][2]; }
cvm::real xx, xy, xz, yx, yy, yz, zx, zy, zz;
/// Default constructor
inline rmatrix()
: cvm::matrix2d<cvm::real>(3, 3)
{}
{
reset();
}
/// Constructor component by component
inline rmatrix(cvm::real xxi, cvm::real xyi, cvm::real xzi,
cvm::real yxi, cvm::real yyi, cvm::real yzi,
cvm::real zxi, cvm::real zyi, cvm::real zzi)
: cvm::matrix2d<cvm::real>(3, 3)
{
this->xx() = xxi;
this->xy() = xyi;
this->xz() = xzi;
this->yx() = yxi;
this->yy() = yyi;
this->yz() = yzi;
this->zx() = zxi;
this->zy() = zyi;
this->zz() = zzi;
xx = xxi;
xy = xyi;
xz = xzi;
yx = yxi;
yy = yyi;
yz = yzi;
zx = zxi;
zy = zyi;
zz = zzi;
}
/// Destructor
inline ~rmatrix()
{}
inline void reset()
{
xx = xy = xz = yx = yy = yz = zx = zy = zz = 0.0;
}
/// Return the determinant
inline cvm::real determinant() const
{
return
( xx() * (yy()*zz() - zy()*yz()))
- (yx() * (xy()*zz() - zy()*xz()))
+ (zx() * (xy()*yz() - yy()*xz()));
( xx * (yy*zz - zy*yz))
- (yx * (xy*zz - zy*xz))
+ (zx * (xy*yz - yy*xz));
}
inline cvm::rmatrix transpose() const
{
return cvm::rmatrix(this->xx(), this->yx(), this->zx(),
this->xy(), this->yy(), this->zy(),
this->xz(), this->yz(), this->zz());
return cvm::rmatrix(xx, yx, zx,
xy, yy, zy,
xz, yz, zz);
}
friend cvm::rvector operator * (cvm::rmatrix const &m, cvm::rvector const &r);
};
inline cvm::rvector operator * (cvm::rmatrix const &m,
inline friend cvm::rvector operator * (cvm::rmatrix const &m,
cvm::rvector const &r)
{
return cvm::rvector(m.xx()*r.x + m.xy()*r.y + m.xz()*r.z,
m.yx()*r.x + m.yy()*r.y + m.yz()*r.z,
m.zx()*r.x + m.zy()*r.y + m.zz()*r.z);
}
{
return cvm::rvector(m.xx*r.x + m.xy*r.y + m.xz*r.z,
m.yx*r.x + m.yy*r.y + m.yz*r.z,
m.zx*r.x + m.zy*r.y + m.zz*r.z);
}
};
@ -1151,11 +1113,6 @@ public:
q0-=h.q0; q1-=h.q1; q2-=h.q2; q3-=h.q3;
}
/// Promote a 3-vector to a quaternion
static inline cvm::quaternion promote(cvm::rvector const &v)
{
return cvm::quaternion(0.0, v.x, v.y, v.z);
}
/// Return the vector component
inline cvm::rvector get_vector() const
{
@ -1207,7 +1164,8 @@ public:
/// reference frame)
inline cvm::rvector rotate(cvm::rvector const &v) const
{
return ((*this) * promote(v) * ((*this).conjugate())).get_vector();
return ( (*this) * cvm::quaternion(0.0, v.x, v.y, v.z) *
this->conjugate() ).get_vector();
}
/// \brief Rotate Q2 through this quaternion (put it in the rotated
@ -1223,18 +1181,18 @@ public:
{
cvm::rmatrix R;
R.xx() = q0*q0 + q1*q1 - q2*q2 - q3*q3;
R.yy() = q0*q0 - q1*q1 + q2*q2 - q3*q3;
R.zz() = q0*q0 - q1*q1 - q2*q2 + q3*q3;
R.xx = q0*q0 + q1*q1 - q2*q2 - q3*q3;
R.yy = q0*q0 - q1*q1 + q2*q2 - q3*q3;
R.zz = q0*q0 - q1*q1 - q2*q2 + q3*q3;
R.xy() = 2.0 * (q1*q2 - q0*q3);
R.xz() = 2.0 * (q0*q2 + q1*q3);
R.xy = 2.0 * (q1*q2 - q0*q3);
R.xz = 2.0 * (q0*q2 + q1*q3);
R.yx() = 2.0 * (q0*q3 + q1*q2);
R.yz() = 2.0 * (q2*q3 - q0*q1);
R.yx = 2.0 * (q0*q3 + q1*q2);
R.yz = 2.0 * (q2*q3 - q0*q1);
R.zx() = 2.0 * (q1*q3 - q0*q2);
R.zy() = 2.0 * (q0*q1 + q2*q3);
R.zx = 2.0 * (q1*q3 - q0*q2);
R.zy = 2.0 * (q0*q1 + q2*q3);
return R;
}

34
src/COLVARS/colvarproxy_lammps.cpp
View File

@ -43,9 +43,10 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
first_timestep=true;
previous_step=-1;
t_target=temp;
do_exit=false;
engine_ready_ = false;
// set input restart name and strip the extension, if present
input_prefix_str = std::string(inp_name ? inp_name : "");
if (input_prefix_str.rfind(".colvars.state") != std::string::npos)
@ -87,7 +88,7 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
}
void colvarproxy_lammps::init(const char *conf_file)
void colvarproxy_lammps::init()
{
version_int = get_version_from_string(COLVARPROXY_VERSION);
@ -102,18 +103,13 @@ void colvarproxy_lammps::init(const char *conf_file)
my_angstrom = _lmp->force->angstrom;
// Front-end unit is the same as back-end
angstrom_value = my_angstrom;
angstrom_value_ = my_angstrom;
// my_kcal_mol = _lmp->force->qe2f / 23.060549;
// force->qe2f is 1eV expressed in LAMMPS' energy unit (1 if unit is eV, 23 if kcal/mol)
my_boltzmann = _lmp->force->boltz;
boltzmann_ = _lmp->force->boltz;
my_timestep = _lmp->update->dt * _lmp->force->femtosecond;
// TODO move one or more of these to setup() if needed
colvars->read_config_file(conf_file);
colvars->setup_input();
colvars->setup_output();
if (_lmp->update->ntimestep != 0) {
cvm::log("Setting initial step number from LAMMPS: "+
cvm::to_str(_lmp->update->ntimestep)+"\n");
@ -123,7 +119,7 @@ void colvarproxy_lammps::init(const char *conf_file)
if (cvm::debug()) {
cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
cvm::log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n");
cvm::log("atoms_refcount = "+cvm::to_str(atoms_refcount)+"\n");
cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n");
cvm::log(cvm::line_marker);
cvm::log("Info: done initializing the colvars proxy object.\n");
@ -154,8 +150,12 @@ colvarproxy_lammps::~colvarproxy_lammps()
// re-initialize data where needed
int colvarproxy_lammps::setup()
{
int error_code = colvarproxy::setup();
my_timestep = _lmp->update->dt * _lmp->force->femtosecond;
return colvars->setup();
error_code |= colvars->update_engine_parameters();
error_code |= colvars->setup_input();
error_code |= colvars->setup_output();
return error_code;
}
// trigger colvars computation
@ -222,17 +222,19 @@ double colvarproxy_lammps::compute()
if (cvm::debug()) {
cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
cvm::log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n");
cvm::log("atoms_refcount = "+cvm::to_str(atoms_refcount)+"\n");
cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n");
cvm::log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n");
}
// call the collective variable module
colvars->calc();
// Call the collective variable module
if (colvars->calc() != COLVARS_OK) {
cvm::error("Error in the collective variables module.\n", COLVARS_ERROR);
}
if (cvm::debug()) {
cvm::log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
cvm::log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n");
cvm::log("atoms_refcount = "+cvm::to_str(atoms_refcount)+"\n");
cvm::log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n");
cvm::log("atoms_new_colvar_forces = "+cvm::to_str(atoms_new_colvar_forces)+"\n");
}
@ -384,7 +386,7 @@ int colvarproxy_lammps::init_atom(int atom_number)
for (size_t i = 0; i < atoms_ids.size(); i++) {
if (atoms_ids[i] == aid) {
// this atom id was already recorded
atoms_ncopies[i] += 1;
atoms_refcount[i] += 1;
return i;
}
}

13
src/COLVARS/colvarproxy_lammps.h
View File

@ -33,7 +33,7 @@ class colvarproxy_lammps : public colvarproxy {
LAMMPS_NS::RanPark *_random;
// state of LAMMPS properties
double t_target, my_timestep, my_boltzmann, my_angstrom;
double my_timestep, my_angstrom;
double bias_energy;
int previous_step;
@ -50,7 +50,7 @@ class colvarproxy_lammps : public colvarproxy {
colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp, const char *, const char *, const int, const double,
MPI_Comm);
~colvarproxy_lammps() override;
void init(const char *);
void init();
int setup() override;
// disable default and copy constructor
@ -60,7 +60,7 @@ class colvarproxy_lammps : public colvarproxy {
// methods for lammps to move data or trigger actions in the proxy
public:
void set_temperature(double t) { t_target = t; };
bool total_forces_enabled() const override { return total_force_requested; };
bool total_forces_same_step() const override { return true; };
bool want_exit() const { return do_exit; };
@ -86,10 +86,6 @@ class colvarproxy_lammps : public colvarproxy {
// Request to set the units used internally by Colvars
int set_unit_system(std::string const &units_in, bool check_only) override;
inline cvm::real backend_angstrom_value() override { return my_angstrom; };
inline cvm::real boltzmann() override { return my_boltzmann; };
inline cvm::real temperature() override { return t_target; };
inline cvm::real dt() override
{
return my_timestep;
@ -101,8 +97,7 @@ class colvarproxy_lammps : public colvarproxy {
void log(std::string const &message) override;
void error(std::string const &message) override;
cvm::rvector position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2) const override;
cvm::rvector position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const override;
cvm::real rand_gaussian(void) override { return _random->gaussian(); };

2
src/COLVARS/colvarproxy_lammps_version.h
View File

@ -1,3 +1,3 @@
#ifndef COLVARPROXY_VERSION
#define COLVARPROXY_VERSION "2022-05-09"
#define COLVARPROXY_VERSION "2023-04-12"
#endif

10
src/COLVARS/fix_colvars.cpp
View File

@ -443,7 +443,9 @@ void FixColvars::one_time_init()
}
proxy = new colvarproxy_lammps(lmp,inp_name,out_name,rng_seed,t_target,root2root);
proxy->init(conf_file);
proxy->init();
proxy->add_config("configfile", conf_file);
proxy->parse_module_config();
num_coords = (proxy->modify_atom_positions()->size());
}
@ -677,16 +679,16 @@ void FixColvars::post_force(int /*vflag*/)
error->one(FLERR,"Run aborted on request from colvars module.\n");
if (!tstat_fix) {
proxy->set_temperature(0.0);
proxy->set_target_temperature(0.0);
} else {
int tmp;
// get thermostat target temperature from corresponding fix,
// if the fix supports extraction.
double *tt = (double *) tstat_fix->extract("t_target", tmp);
if (tt)
proxy->set_temperature(*tt);
proxy->set_target_temperature(*tt);
else
proxy->set_temperature(0.0);
proxy->set_target_temperature(0.0);
}
}