Bugfix for Colvars library (update to version 2019-08-05) (51ba9bd5) · Commits · 郑智淋 / lammps

lib/colvars/colvaratoms.cpp

+31 −11

Original line number	Diff line number	Diff line
		@@ -178,6 +178,31 @@ int cvm::atom_group::remove_atom(cvm::atom_iter ai)
		}


		int cvm::atom_group::set_dummy()
		{
		if (atoms_ids.size() > 0) {
		return cvm::error("Error: setting group with keyword \""+key+
		"\" and name \""+name+"\" as dummy, but it already "
		"contains atoms.\n", INPUT_ERROR);
		}
		b_dummy = true;
		return COLVARS_OK;
		}


		int cvm::atom_group::set_dummy_pos(cvm::atom_pos const &pos)
		{
		if (b_dummy) {
		dummy_atom_pos = pos;
		} else {
		return cvm::error("Error: setting dummy position for group with keyword \""+
		key+"\" and name \""+name+
		"\", but it is not dummy.\n", INPUT_ERROR);
		}
		return COLVARS_OK;
		}


		int cvm::atom_group::init()
		{
		if (!key.size()) key = "unnamed";
		@@ -469,19 +494,14 @@ int cvm::atom_group::parse(std::string const &group_conf)
		// checks of doubly-counted atoms have been handled by add_atom() already

		if (get_keyval(group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos())) {
		b_dummy = true;
		// note: atoms_ids.size() is used here in lieu of atoms.size(),
		// which can be empty for scalable groups
		if (atoms_ids.size()) {
		cvm::error("Error: cannot set up group \""+
		key+"\" as a dummy atom "
		"and provide it with atom definitions.\n", INPUT_ERROR);
		}

		parse_error \|= set_dummy();
		parse_error \|= set_dummy_pos(dummy_atom_pos);

		} else {
		b_dummy = false;

		if (!(atoms_ids.size())) {
		cvm::error("Error: no atoms defined for atom group \""+
		parse_error \|= cvm::error("Error: no atoms defined for atom group \""+
		key+"\".\n", INPUT_ERROR);
		}

lib/colvars/colvaratoms.h

+6 −0

Original line number	Diff line number	Diff line
		@@ -207,6 +207,12 @@ public:
		/// \brief Remove an atom object from this group
		int remove_atom(cvm::atom_iter ai);

		/// Set this group as a dummy group (no actual atoms)
		int set_dummy();

		/// If this group is dummy, set the corresponding position
		int set_dummy_pos(cvm::atom_pos const &pos);

		/// \brief Print the updated the total mass and charge of a group.
		/// This is needed in case the hosting MD code has an option to
		/// change atom masses after their initialization.

lib/colvars/colvarcomp.h

+6 −4

Original line number	Diff line number	Diff line
		@@ -887,9 +887,8 @@ protected:
		/// Integer exponent of the function denominator
		int ed;

		/// \brief If true, group2 will be treated as a single atom, stored in this
		/// accessory group
		cvm::atom_group *group2_center;
		/// If true, group2 will be treated as a single atom
		bool b_group2_center_only;

		/// Tolerance for the pair list
		cvm::real tolerance;
		@@ -941,9 +940,12 @@ public:
		bool **pairlist_elem,
		cvm::real tolerance);

		/// Main workhorse function
		/// Workhorse function
		template<int flags> int compute_coordnum();

		/// Workhorse function
		template<int flags> void main_loop(bool *pairlist_elem);

		};

lib/colvars/colvarcomp_coordnums.cpp

+36 −81

Original line number	Diff line number	Diff line
		@@ -91,7 +91,7 @@ cvm::real colvar::coordnum::switching_function(cvm::real const &r0,


		colvar::coordnum::coordnum(std::string const &conf)
		: cvc(conf), b_anisotropic(false), group2_center(NULL), pairlist(NULL)
		: cvc(conf), b_anisotropic(false), pairlist(NULL)

		{
		function_type = "coordnum";
		@@ -156,14 +156,7 @@ colvar::coordnum::coordnum(std::string const &conf)
		cvm::log("Warning: only minimum-image distances are used by this variable.\n");
		}

		bool b_group2_center_only = false;
		get_keyval(conf, "group2CenterOnly", b_group2_center_only, group2->b_dummy);
		if (b_group2_center_only) {
		if (!group2_center) {
		group2_center = new cvm::atom_group();
		group2_center->add_atom(cvm::atom());
		}
		}

		get_keyval(conf, "tolerance", tolerance, 0.0);
		if (tolerance > 0) {
		@@ -185,7 +178,7 @@ colvar::coordnum::coordnum(std::string const &conf)


		colvar::coordnum::coordnum()
		: b_anisotropic(false), group2_center(NULL), pairlist(NULL)
		: b_anisotropic(false), pairlist(NULL)
		{
		function_type = "coordnum";
		x.type(colvarvalue::type_scalar);
		@@ -197,69 +190,60 @@ colvar::coordnum::~coordnum()
		if (pairlist != NULL) {
		delete [] pairlist;
		}
		if (group2_center != NULL) {
		delete group2_center;
		}
		}


		template<int compute_flags> int colvar::coordnum::compute_coordnum()
		template<int flags> void colvar::coordnum::main_loop(bool **pairlist_elem)
		{
		if (group2_center) {
		(*group2_center)[0].pos = group2->center_of_mass();
		group2_center->calc_required_properties();
		if (b_group2_center_only) {
		cvm::atom group2_com_atom;
		group2_com_atom.pos = group2->center_of_mass();
		for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
		x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
		*ai1, group2_com_atom,
		pairlist_elem,
		tolerance);
		}
		if (b_group2_center_only) {
		group2->set_weighted_gradient(group2_com_atom.grad);
		}
		} else {
		for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
		for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
		x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
		ai1, ai2,
		pairlist_elem,
		tolerance);
		}
		}
		}
		}
		cvm::atom_group *group2p = group2_center ? group2_center : group2;


		template<int compute_flags> int colvar::coordnum::compute_coordnum()
		{
		bool const use_pairlist = (pairlist != NULL);
		bool const rebuild_pairlist = (pairlist != NULL) &&
		(cvm::step_relative() % pairlist_freq == 0);

		bool *pairlist_elem = use_pairlist ? pairlist : NULL;
		cvm::atom_iter ai1 = group1->begin(), ai2 = group2p->begin();
		cvm::atom_iter const ai1_end = group1->end();
		cvm::atom_iter const ai2_end = group2p->end();

		if (b_anisotropic) {

		if (use_pairlist) {

		if (rebuild_pairlist) {

		int const flags = compute_flags \| ef_anisotropic \| ef_use_pairlist \|
		ef_rebuild_pairlist;
		for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
		for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
		x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
		ai1, ai2,
		&pairlist_elem,
		tolerance);
		}
		}

		main_loop<flags>(&pairlist_elem);
		} else {

		int const flags = compute_flags \| ef_anisotropic \| ef_use_pairlist;
		for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
		for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
		x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
		ai1, ai2,
		&pairlist_elem,
		tolerance);
		}
		}
		main_loop<flags>(&pairlist_elem);
		}

		} else { // if (use_pairlist) {
		} else {

		int const flags = compute_flags \| ef_anisotropic;
		for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
		for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
		x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
		ai1, ai2,
		NULL, 0.0);
		}
		}
		main_loop<flags>(NULL);
		}

		} else {
		@@ -267,46 +251,17 @@ template<int compute_flags> int colvar::coordnum::compute_coordnum()
		if (use_pairlist) {

		if (rebuild_pairlist) {

		int const flags = compute_flags \| ef_use_pairlist \| ef_rebuild_pairlist;
		for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
		for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
		x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
		ai1, ai2,
		&pairlist_elem,
		tolerance);
		}
		}

		main_loop<flags>(&pairlist_elem);
		} else {

		int const flags = compute_flags \| ef_use_pairlist;
		for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
		for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
		x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
		ai1, ai2,
		&pairlist_elem,
		tolerance);
		}
		}
		main_loop<flags>(&pairlist_elem);
		}

		} else { // if (use_pairlist) {
		} else {

		int const flags = compute_flags;
		for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
		for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
		x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
		ai1, ai2,
		NULL, 0.0);
		}
		}
		}
		}

		if (compute_flags & ef_gradients) {
		if (group2_center) {
		group2->set_weighted_gradient((*group2_center)[0].grad);
		main_loop<flags>(NULL);
		}
		}

lib/colvars/colvars_version.h

+1 −1

Original line number	Diff line number	Diff line
		#ifndef COLVARS_VERSION
		#define COLVARS_VERSION "2019-08-01"
		#define COLVARS_VERSION "2019-08-05"
		// 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

Admin message