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lammps/lib/colvars/colvaratoms.cpp
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colvaratoms.cpp
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#include "colvarmodule.h"
#include "colvarparse.h"
#include "colvaratoms.h"
// atom member functions depend tightly on the MD interface, and are
// thus defined in colvarproxy_xxx.cpp
// atom_group member functions
cvm::atom_group::atom_group (std::string const &conf,
char const *key,
atom_group *ref_pos_group_in)
: b_center (false), b_rotate (false),
ref_pos_group (NULL), // this is always set within parse(),
// regardless of ref_pos_group_in
noforce (false)
{
cvm::log ("Defining atom group \""+
std::string (key)+"\".\n");
parse (conf, key, ref_pos_group_in);
}
void cvm::atom_group::parse (std::string const &conf,
char const *key,
atom_group *ref_pos_group_in)
{
std::string group_conf;
// save_delimiters is set to false for this call, because "conf" is
// not the config string of this group, but of its parent object
// (which has already taken care of the delimiters)
save_delimiters = false;
key_lookup (conf, key, group_conf, dummy_pos);
// restoring the normal value, because we do want keywords checked
// inside "group_conf"
save_delimiters = true;
if (group_conf.size() == 0) {
cvm::fatal_error ("Error: atom group \""+
std::string (key)+"\" is set, but "
"has no definition.\n");
}
cvm::increase_depth();
cvm::log ("Initializing atom group \""+std::string (key)+"\".\n");
// whether or not to include messages in the log
colvarparse::Parse_Mode mode = parse_silent;
{
bool b_verbose;
get_keyval (group_conf, "verboseOutput", b_verbose, false, parse_silent);
if (b_verbose) mode = parse_normal;
}
{
// get the atoms by numbers
std::vector<int> atom_indexes;
if (get_keyval (group_conf, "atomNumbers", atom_indexes, atom_indexes, mode)) {
if (atom_indexes.size()) {
this->reserve (this->size()+atom_indexes.size());
for (size_t i = 0; i < atom_indexes.size(); i++) {
this->push_back (cvm::atom (atom_indexes[i]));
}
} else
cvm::fatal_error ("Error: no numbers provided for \""
"atomNumbers\".\n");
}
}
{
std::string range_conf = "";
size_t pos = 0;
while (key_lookup (group_conf, "atomNumbersRange",
range_conf, pos)) {
if (range_conf.size()) {
std::istringstream is (range_conf);
int initial, final;
char dash;
if ( (is >> initial) && (initial > 0) &&
(is >> dash) && (dash == '-') &&
(is >> final) && (final > 0) ) {
for (int anum = initial; anum <= final; anum++) {
this->push_back (cvm::atom (anum));
}
range_conf = "";
continue;
}
}
cvm::fatal_error ("Error: no valid definition for \""
"atomNumbersRange\", \""+
range_conf+"\".\n");
}
}
std::vector<std::string> psf_segids;
get_keyval (group_conf, "psfSegID", psf_segids, std::vector<std::string> (), mode);
for (std::vector<std::string>::iterator psii = psf_segids.begin();
psii < psf_segids.end(); psii++) {
if ( (psii->size() == 0) || (psii->size() > 4) ) {
cvm::fatal_error ("Error: invalid segmend identifier provided, \""+
(*psii)+"\".\n");
}
}
{
std::string range_conf = "";
size_t pos = 0;
size_t range_count = 0;
std::vector<std::string>::iterator psii = psf_segids.begin();
while (key_lookup (group_conf, "atomNameResidueRange",
range_conf, pos)) {
if (psii > psf_segids.end()) {
cvm::fatal_error ("Error: more instances of \"atomNameResidueRange\" than "
"values of \"psfSegID\".\n");
}
std::string const &psf_segid = psf_segids.size() ? *psii : std::string ("");
if (range_conf.size()) {
std::istringstream is (range_conf);
std::string atom_name;
int initial, final;
char dash;
if ( (is >> atom_name) && (atom_name.size()) &&
(is >> initial) && (initial > 0) &&
(is >> dash) && (dash == '-') &&
(is >> final) && (final > 0) ) {
for (int resid = initial; resid <= final; resid++) {
this->push_back (cvm::atom (resid, atom_name, psf_segid));
}
range_conf = "";
} else {
cvm::fatal_error ("Error: cannot parse definition for \""
"atomNameResidueRange\", \""+
range_conf+"\".\n");
}
} else {
cvm::fatal_error ("Error: atomNameResidueRange with empty definition.\n");
}
if (psf_segid.size())
psii++;
}
}
{
// read the atoms from a file
std::string atoms_file_name;
if (get_keyval (group_conf, "atomsFile", atoms_file_name, std::string (""), mode)) {
std::string atoms_col;
if (!get_keyval (group_conf, "atomsCol", atoms_col, std::string (""), mode)) {
cvm::fatal_error ("Error: parameter atomsCol is required if atomsFile is set.\n");
}
double atoms_col_value;
bool const atoms_col_value_defined = get_keyval (group_conf, "atomsColValue", atoms_col_value, 0.0, mode);
if (atoms_col_value_defined && (!atoms_col_value))
cvm::fatal_error ("Error: atomsColValue, "
"if provided, must be non-zero.\n");
cvm::load_atoms (atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
}
}
for (std::vector<cvm::atom>::iterator a1 = this->begin();
a1 != this->end(); a1++) {
std::vector<cvm::atom>::iterator a2 = a1;
++a2;
for ( ; a2 != this->end(); a2++) {
if (a1->id == a2->id) {
if (cvm::debug())
cvm::log ("Discarding doubly counted atom with number "+
cvm::to_str (a1->id+1)+".\n");
a2 = this->erase (a2);
if (a2 == this->end())
break;
}
}
}
if (get_keyval (group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos(), mode)) {
b_dummy = true;
this->total_mass = 1.0;
} else
b_dummy = false;
if (b_dummy && (this->size()))
cvm::fatal_error ("Error: cannot set up group \""+
std::string (key)+"\" as a dummy atom "
"and provide it with atom definitions.\n");
#if (! defined (COLVARS_STANDALONE))
if ( (!b_dummy) && (!cvm::b_analysis) && (!(this->size())) ) {
cvm::fatal_error ("Error: no atoms defined for atom group \""+
std::string (key)+"\".\n");
}
#endif
if (!b_dummy) {
this->total_mass = 0.0;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
this->total_mass += ai->mass;
}
}
get_keyval (group_conf, "disableForces", noforce, false, mode);
get_keyval (group_conf, "centerReference", b_center, false, mode);
get_keyval (group_conf, "rotateReference", b_rotate, false, mode);
if (b_center || b_rotate) {
if (b_dummy)
cvm::fatal_error ("Error: cannot set \"centerReference\" or "
"\"rotateReference\" with \"dummyAtom\".\n");
// use refPositionsGroup instead of this group as the one which is
// used to fit the coordinates
if (key_lookup (group_conf, "refPositionsGroup")) {
if (ref_pos_group) {
cvm::fatal_error ("Error: the atom group \""+
std::string (key)+"\" has already a reference group "
"for the rototranslational fit, which was communicated by the "
"colvar component. You should not use refPositionsGroup "
"in this case.\n");
}
cvm::log ("Within atom group \""+std::string (key)+"\":\n");
ref_pos_group = new atom_group (group_conf, "refPositionsGroup");
}
atom_group *ag = ref_pos_group ? ref_pos_group : this;
if (get_keyval (group_conf, "refPositions", ref_pos, ref_pos, mode)) {
cvm::log ("Using reference positions from input file.\n");
if (ref_pos.size() != ag->size()) {
cvm::fatal_error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms within \""+
std::string (key)+
"\" ("+cvm::to_str (ag->size())+").\n");
}
}
std::string ref_pos_file;
if (get_keyval (group_conf, "refPositionsFile", ref_pos_file, std::string (""), mode)) {
if (ref_pos.size()) {
cvm::fatal_error ("Error: cannot specify \"refPositionsFile\" and "
"\"refPositions\" at the same time.\n");
}
std::string ref_pos_col;
double ref_pos_col_value;
if (get_keyval (group_conf, "refPositionsCol", ref_pos_col, std::string (""), mode)) {
// if provided, use PDB column to select coordinates
bool found = get_keyval (group_conf, "refPositionsColValue", ref_pos_col_value, 0.0, mode);
if (found && !ref_pos_col_value)
cvm::fatal_error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
} else {
// if not, rely on existing atom indices for the group
ag->create_sorted_ids();
}
cvm::load_coords (ref_pos_file.c_str(), ref_pos, ag->sorted_ids,
ref_pos_col, ref_pos_col_value);
}
if (ref_pos.size()) {
if (b_rotate) {
if (ref_pos.size() != ag->size())
cvm::fatal_error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms within \""+
std::string (key)+
"\" ("+cvm::to_str (ag->size())+").\n");
}
// save the center of mass of ref_pos and then subtract it from
// them; in this way it is possible to use the coordinates for
// the rotational fit, if needed
ref_pos_cog = cvm::atom_pos (0.0, 0.0, 0.0);
std::vector<cvm::atom_pos>::iterator pi = ref_pos.begin();
for ( ; pi != ref_pos.end(); pi++) {
ref_pos_cog += *pi;
}
ref_pos_cog /= (cvm::real) ref_pos.size();
for (std::vector<cvm::atom_pos>::iterator pi = ref_pos.begin();
pi != ref_pos.end(); pi++) {
(*pi) -= ref_pos_cog;
}
} else {
#if (! defined (COLVARS_STANDALONE))
if (!cvm::b_analysis)
cvm::fatal_error ("Error: no reference positions provided.\n");
#endif
}
if (b_rotate && !noforce) {
cvm::log ("Warning: atom group \""+std::string (key)+
"\" is set to be rotated to a reference orientation: "
"a torque different than zero on this group "
"could make the simulation unstable. "
"If this happens, set \"disableForces\" to yes "
"for this group.\n");
}
}
if (cvm::debug())
cvm::log ("Done initializing atom group with name \""+
std::string (key)+"\".\n");
this->check_keywords (group_conf, key);
cvm::log ("Atom group \""+std::string (key)+"\" defined, "+
cvm::to_str (this->size())+" initialized: total mass = "+
cvm::to_str (this->total_mass)+".\n");
cvm::decrease_depth();
}
cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
: b_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), noforce (false)
{
this->reserve (atoms.size());
for (size_t i = 0; i < atoms.size(); i++) {
this->push_back (atoms[i]);
}
total_mass = 0.0;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
total_mass += ai->mass;
}
}
cvm::atom_group::atom_group()
: b_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), noforce (false)
{
total_mass = 0.0;
}
cvm::atom_group::~atom_group()
{
if (ref_pos_group) {
delete ref_pos_group;
ref_pos_group = NULL;
}
}
void cvm::atom_group::add_atom (cvm::atom const &a)
{
if (b_dummy) {
cvm::fatal_error ("Error: cannot add atoms to a dummy group.\n");
} else {
this->push_back (a);
total_mass += a.mass;
}
}
void cvm::atom_group::create_sorted_ids (void)
{
// Only do the work if the vector is not yet populated
if (sorted_ids.size())
return;
std::list<int> temp_id_list;
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
temp_id_list.push_back (ai->id);
}
temp_id_list.sort();
temp_id_list.unique();
if (temp_id_list.size() != this->size()) {
cvm::fatal_error ("Error: duplicate atom IDs in atom group? (found " +
cvm::to_str(temp_id_list.size()) +
" unique atom IDs instead of" +
cvm::to_str(this->size()) + ").\n");
}
sorted_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
return;
}
void cvm::atom_group::read_positions()
{
if (b_dummy) return;
#if (! defined (COLVARS_STANDALONE))
if (!this->size())
cvm::fatal_error ("Error: no atoms defined in the requested group.\n");
#endif
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_position();
}
if (ref_pos_group)
ref_pos_group->read_positions();
atom_group *fit_group = ref_pos_group ? ref_pos_group : this;
if (b_center) {
// store aside the current center of geometry (all positions will be
// set to the closest images to the first one) and then center on
// the origin
cvm::atom_pos const cog = fit_group->center_of_geometry();
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos -= cog;
}
}
if (b_rotate) {
// rotate the group (around the center of geometry if b_center is
// true, around the origin otherwise); store the rotation, in
// order to bring back the forces to the original frame before
// applying them
rot.calc_optimal_rotation (fit_group->positions(), ref_pos);
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos = rot.rotate (ai->pos);
}
}
if (b_center) {
// use the center of geometry of ref_pos
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos += ref_pos_cog;
}
}
}
void cvm::atom_group::apply_translation (cvm::rvector const &t)
{
if (b_dummy) return;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos += t;
}
}
void cvm::atom_group::apply_rotation (cvm::rotation const &rot)
{
if (b_dummy) return;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->pos = rot.rotate (ai->pos);
}
}
void cvm::atom_group::read_velocities()
{
if (b_dummy) return;
if (b_rotate) {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_velocity();
ai->vel = rot.rotate (ai->vel);
}
} else {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_velocity();
}
}
}
void cvm::atom_group::read_system_forces()
{
if (b_dummy) return;
if (b_rotate) {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_system_force();
ai->system_force = rot.rotate (ai->system_force);
}
} else {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->read_system_force();
}
}
}
cvm::atom_pos cvm::atom_group::center_of_geometry (cvm::atom_pos const &ref_pos)
{
if (b_dummy) {
cvm::select_closest_image (dummy_atom_pos, ref_pos);
return dummy_atom_pos;
}
cvm::atom_pos cog (0.0, 0.0, 0.0);
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
cvm::select_closest_image (ai->pos, ref_pos);
cog += ai->pos;
}
cog /= this->size();
return cog;
}
cvm::atom_pos cvm::atom_group::center_of_geometry() const
{
if (b_dummy)
return dummy_atom_pos;
cvm::atom_pos cog (0.0, 0.0, 0.0);
for (cvm::atom_const_iter ai = this->begin();
ai != this->end(); ai++) {
cog += ai->pos;
}
cog /= this->size();
return cog;
}
cvm::atom_pos cvm::atom_group::center_of_mass (cvm::atom_pos const &ref_pos)
{
if (b_dummy) {
cvm::select_closest_image (dummy_atom_pos, ref_pos);
return dummy_atom_pos;
}
cvm::atom_pos com (0.0, 0.0, 0.0);
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
cvm::select_closest_image (ai->pos, ref_pos);
com += ai->mass * ai->pos;
}
com /= this->total_mass;
return com;
}
cvm::atom_pos cvm::atom_group::center_of_mass() const
{
if (b_dummy)
return dummy_atom_pos;
cvm::atom_pos com (0.0, 0.0, 0.0);
for (cvm::atom_const_iter ai = this->begin();
ai != this->end(); ai++) {
com += ai->mass * ai->pos;
}
com /= this->total_mass;
return com;
}
void cvm::atom_group::set_weighted_gradient (cvm::rvector const &grad)
{
if (b_dummy) return;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->grad = (ai->mass/this->total_mass) * grad;
}
}
std::vector<cvm::atom_pos> cvm::atom_group::positions() const
{
if (b_dummy)
cvm::fatal_error ("Error: positions are not available "
"from a dummy atom group.\n");
std::vector<cvm::atom_pos> x (this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator xi = x.begin();
for ( ; ai != this->end(); xi++, ai++) {
*xi = ai->pos;
}
return x;
}
std::vector<cvm::atom_pos> cvm::atom_group::positions_shifted (cvm::rvector const &shift) const
{
if (b_dummy)
cvm::fatal_error ("Error: positions are not available "
"from a dummy atom group.\n");
std::vector<cvm::atom_pos> x (this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator xi = x.begin();
for ( ; ai != this->end(); xi++, ai++) {
*xi = (ai->pos + shift);
}
return x;
}
std::vector<cvm::rvector> cvm::atom_group::velocities() const
{
if (b_dummy)
cvm::fatal_error ("Error: velocities are not available "
"from a dummy atom group.\n");
std::vector<cvm::rvector> v (this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator vi = v.begin();
for ( ; ai != this->end(); vi++, ai++) {
*vi = ai->vel;
}
return v;
}
std::vector<cvm::rvector> cvm::atom_group::system_forces() const
{
if (b_dummy)
cvm::fatal_error ("Error: system forces are not available "
"from a dummy atom group.\n");
std::vector<cvm::rvector> f (this->size(), 0.0);
cvm::atom_const_iter ai = this->begin();
std::vector<cvm::atom_pos>::iterator fi = f.begin();
for ( ; ai != this->end(); fi++, ai++) {
*fi = ai->system_force;
}
return f;
}
cvm::rvector cvm::atom_group::system_force() const
{
if (b_dummy)
cvm::fatal_error ("Error: system forces are not available "
"from a dummy atom group.\n");
cvm::rvector f (0.0);
for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
f += ai->system_force;
}
return f;
}
void cvm::atom_group::apply_colvar_force (cvm::real const &force)
{
if (b_dummy)
return;
if (noforce)
cvm::fatal_error ("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
if (b_rotate) {
// get the forces back from the rotated frame
cvm::rotation const rot_inv = rot.inverse();
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force (rot_inv.rotate (force * ai->grad));
}
} else {
// no need to manipulate gradients, they are still in the original
// frame
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force (force * ai->grad);
}
}
}
void cvm::atom_group::apply_force (cvm::rvector const &force)
{
if (b_dummy)
return;
if (noforce)
cvm::fatal_error ("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
if (b_rotate) {
cvm::rotation const rot_inv = rot.inverse();
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force (rot_inv.rotate ((ai->mass/this->total_mass) * force));
}
} else {
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force ((ai->mass/this->total_mass) * force);
}
}
}
void cvm::atom_group::apply_forces (std::vector<cvm::rvector> const &forces)
{
if (b_dummy)
return;
if (noforce)
cvm::fatal_error ("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
if (forces.size() != this->size()) {
cvm::fatal_error ("Error: trying to apply an array of forces to an atom "
"group which does not have the same length.\n");
}
if (b_rotate) {
cvm::rotation const rot_inv = rot.inverse();
cvm::atom_iter ai = this->begin();
std::vector<cvm::rvector>::const_iterator fi = forces.begin();
for ( ; ai != this->end(); fi++, ai++) {
ai->apply_force (rot_inv.rotate (*fi));
}
} else {
cvm::atom_iter ai = this->begin();
std::vector<cvm::rvector>::const_iterator fi = forces.begin();
for ( ; ai != this->end(); fi++, ai++) {
ai->apply_force (*fi);
}
}
}
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