ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14829 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2016-04-15 16:07:01 +00:00
parent 32509da721
commit 212a955285
31 changed files with 1713 additions and 1493 deletions
Download Patch File Download Diff File Expand all files Collapse all files

141
lib/colvars/colvaratoms.cpp
View File

@ -4,7 +4,6 @@
#include "colvarparse.h"
#include "colvaratoms.h"
cvm::atom::atom()
{
index = -1;
@ -68,8 +67,7 @@ cvm::atom_group::atom_group(std::string const &conf,
char const *key_in)
{
key = key_in;
cvm::log("Defining atom group \""+
std::string(key)+"\".\n");
cvm::log("Defining atom group \"" + key + "\".\n");
init();
// real work is done by parse
parse(conf);
@ -93,8 +91,9 @@ cvm::atom_group::atom_group()
cvm::atom_group::~atom_group()
{
if (index >= 0) {
if (is_enabled(f_ag_scalable)) {
(cvm::proxy)->clear_atom_group(index);
index = -1;
}
if (ref_pos_group) {
@ -151,7 +150,7 @@ int cvm::atom_group::add_atom_id(int aid)
int cvm::atom_group::remove_atom(cvm::atom_iter ai)
{
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: cannot remove atoms from a scalable group.\n", INPUT_ERROR);
return COLVARS_ERROR;
}
@ -173,10 +172,11 @@ int cvm::atom_group::remove_atom(cvm::atom_iter ai)
int cvm::atom_group::init()
{
if (!key.size()) key = "atoms";
atoms.clear();
b_scalable = false;
// TODO: check with proxy whether atom forces etc are available
init_ag_requires();
index = -1;
b_center = false;
@ -216,7 +216,7 @@ void cvm::atom_group::update_total_mass()
return;
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
total_mass = (cvm::proxy)->get_atom_group_mass(index);
} else {
total_mass = 0.0;
@ -243,7 +243,7 @@ void cvm::atom_group::update_total_charge()
return;
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
total_charge = (cvm::proxy)->get_atom_group_charge(index);
} else {
total_charge = 0.0;
@ -280,6 +280,8 @@ int cvm::atom_group::parse(std::string const &conf)
cvm::log("Initializing atom group \""+key+"\".\n");
description = "atom group " + key;
// whether or not to include messages in the log
// colvarparse::Parse_Mode mode = parse_silent;
// {
@ -291,9 +293,6 @@ int cvm::atom_group::parse(std::string const &conf)
int parse_error = COLVARS_OK;
// if the cvc allows it, the flag has been set to true by default
get_keyval(group_conf, "scalable", b_scalable, b_scalable);
{
std::string numbers_conf = "";
size_t pos = 0;
@ -373,11 +372,7 @@ int cvm::atom_group::parse(std::string const &conf)
}
// Catch any errors from all the initialization steps above
if (parse_error || cvm::get_error()) return COLVARS_ERROR;
if (b_scalable) {
index = (cvm::proxy)->init_atom_group(atoms_ids);
}
if (parse_error || cvm::get_error()) return (parse_error || cvm::get_error());
// checks of doubly-counted atoms have been handled by add_atom() already
@ -408,6 +403,10 @@ int cvm::atom_group::parse(std::string const &conf)
}
}
if (is_enabled(f_ag_scalable) && !b_dummy) {
index = (cvm::proxy)->init_atom_group(atoms_ids);
}
parse_error |= parse_fitting_options(group_conf);
// TODO move this to colvarparse object
@ -449,7 +448,7 @@ int cvm::atom_group::add_atom_numbers(std::string const &numbers_conf)
if (atom_indexes.size()) {
atoms_ids.reserve(atoms_ids.size()+atom_indexes.size());
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
for (size_t i = 0; i < atom_indexes.size(); i++) {
add_atom_id((cvm::proxy)->check_atom_id(atom_indexes[i]));
}
@ -490,7 +489,7 @@ int cvm::atom_group::add_index_group(std::string const &index_group_name)
atoms_ids.reserve(atoms_ids.size()+index_groups_i->size());
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
for (size_t i = 0; i < index_groups_i->size(); i++) {
add_atom_id((cvm::proxy)->check_atom_id((*index_groups_i)[i]));
}
@ -520,7 +519,7 @@ int cvm::atom_group::add_atom_numbers_range(std::string const &range_conf)
atoms_ids.reserve(atoms_ids.size() + (final - initial + 1));
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
for (int anum = initial; anum <= final; anum++) {
add_atom_id((cvm::proxy)->check_atom_id(anum));
}
@ -558,7 +557,7 @@ int cvm::atom_group::add_atom_name_residue_range(std::string const &psf_segid,
atoms_ids.reserve(atoms_ids.size() + (final - initial + 1));
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
for (int resid = initial; resid <= final; resid++) {
add_atom_id((cvm::proxy)->check_atom_id(resid, atom_name, psf_segid));
}
@ -750,15 +749,24 @@ void cvm::atom_group::read_positions()
int cvm::atom_group::calc_required_properties()
{
if (b_dummy) return COLVARS_OK;
// TODO check if the com is needed?
calc_center_of_mass();
if (!b_scalable) {
// TODO check if calc_center_of_geometry() is needed without a fit?
calc_center_of_geometry();
calc_center_of_geometry();
if (!is_enabled(f_ag_scalable)) {
if (b_center || b_rotate) {
if (ref_pos_group) {
ref_pos_group->calc_center_of_geometry();
}
calc_apply_roto_translation();
// update COM and COG after fitting
calc_center_of_geometry();
calc_center_of_mass();
if (ref_pos_group) {
ref_pos_group->calc_center_of_geometry();
}
}
}
@ -767,37 +775,49 @@ int cvm::atom_group::calc_required_properties()
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void cvm::atom_group::calc_apply_roto_translation()
{
atom_group *fit_group = ref_pos_group ? ref_pos_group : this;
if (b_center) {
// center on the origin first
cvm::atom_pos const cog = fit_group->center_of_geometry();
cvm::atom_pos const cog = ref_pos_group ?
ref_pos_group->center_of_geometry() : this->center_of_geometry();
apply_translation(-1.0 * cog);
if (ref_pos_group) {
ref_pos_group->apply_translation(-1.0 * cog);
}
}
if (b_rotate) {
// rotate the group (around the center of geometry if b_center is
// true, around the origin otherwise)
rot.calc_optimal_rotation(fit_group->positions(), ref_pos);
rot.calc_optimal_rotation(ref_pos_group ?
ref_pos_group->positions() :
this->positions(),
ref_pos);
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
cvm::atom_iter ai;
for (ai = this->begin(); ai != this->end(); ai++) {
ai->pos = rot.rotate(ai->pos);
}
if (ref_pos_group) {
for (ai = ref_pos_group->begin(); ai != ref_pos_group->end(); ai++) {
ai->pos = rot.rotate(ai->pos);
}
}
}
if (b_center) {
// align with the center of geometry of ref_pos
apply_translation(ref_pos_cog);
// update the center of geometry for external use
cog = ref_pos_cog;
if (ref_pos_group) {
ref_pos_group->apply_translation(ref_pos_cog);
}
}
// recalculate the center of mass
calc_center_of_mass();
// update of COM and COG is done from the calling routine
}
void cvm::atom_group::apply_translation(cvm::rvector const &t)
{
if (b_dummy) {
@ -805,7 +825,7 @@ void cvm::atom_group::apply_translation(cvm::rvector const &t)
return;
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: cannot translate the coordinates of a scalable atom group.\n", INPUT_ERROR);
return;
}
@ -815,23 +835,6 @@ void cvm::atom_group::apply_translation(cvm::rvector const &t)
}
}
void cvm::atom_group::apply_rotation(cvm::rotation const &rot)
{
if (b_dummy) {
cvm::error("Error: cannot rotate the coordinates of a dummy atom group.\n", INPUT_ERROR);
return;
}
if (b_scalable) {
cvm::error("Error: cannot rotate the coordinates of a scalable atom group.\n", INPUT_ERROR);
return;
}
for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
ai->pos = rot.rotate(ai->pos - center_of_geometry()) + center_of_geometry();
}
}
void cvm::atom_group::read_velocities()
{
@ -852,6 +855,8 @@ void cvm::atom_group::read_velocities()
}
}
// TODO make this a calc function
void cvm::atom_group::read_system_forces()
{
if (b_dummy) return;
@ -891,7 +896,10 @@ int cvm::atom_group::calc_center_of_mass()
{
if (b_dummy) {
com = dummy_atom_pos;
} else if (b_scalable) {
if (cvm::debug()) {
cvm::log("Dummy atom center of mass = "+cvm::to_str(com)+"\n");
}
} else if (is_enabled(f_ag_scalable)) {
com = (cvm::proxy)->get_atom_group_com(index);
} else {
com.reset();
@ -922,7 +930,7 @@ void cvm::atom_group::set_weighted_gradient(cvm::rvector const &grad)
{
if (b_dummy) return;
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
scalar_com_gradient = grad;
return;
}
@ -993,7 +1001,7 @@ std::vector<cvm::atom_pos> cvm::atom_group::positions() const
"from a dummy atom group.\n", INPUT_ERROR);
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: atomic positions are not available "
"from a scalable atom group.\n", INPUT_ERROR);
}
@ -1014,7 +1022,7 @@ std::vector<cvm::atom_pos> cvm::atom_group::positions_shifted(cvm::rvector const
"from a dummy atom group.\n", INPUT_ERROR);
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: atomic positions are not available "
"from a scalable atom group.\n", INPUT_ERROR);
}
@ -1035,7 +1043,7 @@ std::vector<cvm::rvector> cvm::atom_group::velocities() const
"from a dummy atom group.\n", INPUT_ERROR);
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: atomic velocities are not available "
"from a scalable atom group.\n", INPUT_ERROR);
}
@ -1056,7 +1064,7 @@ std::vector<cvm::rvector> cvm::atom_group::system_forces() const
"from a dummy atom group.\n", INPUT_ERROR);
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
cvm::error("Error: atomic system forces are not available "
"from a scalable atom group.\n", INPUT_ERROR);
}
@ -1070,6 +1078,8 @@ std::vector<cvm::rvector> cvm::atom_group::system_forces() const
return f;
}
// TODO make this an accessor
cvm::rvector cvm::atom_group::system_force() const
{
if (b_dummy) {
@ -1077,7 +1087,7 @@ cvm::rvector cvm::atom_group::system_force() const
"from a dummy atom group.\n", INPUT_ERROR);
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
return (cvm::proxy)->get_atom_group_system_force(index);
}
@ -1104,7 +1114,7 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force)
return;
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
(cvm::proxy)->apply_atom_group_force(index, force * scalar_com_gradient);
return;
}
@ -1156,7 +1166,7 @@ void cvm::atom_group::apply_force(cvm::rvector const &force)
return;
}
if (b_scalable) {
if (is_enabled(f_ag_scalable)) {
(cvm::proxy)->apply_atom_group_force(index, force);
}
@ -1209,3 +1219,8 @@ void cvm::atom_group::apply_forces(std::vector<cvm::rvector> const &forces)
}
}
// Static members
std::vector<cvm::deps::feature *> cvm::atom_group::ag_features;