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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12612 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-10-07 20:30:25 +00:00
parent 3c0612815f
commit 044084847b
33 changed files with 2284 additions and 2595 deletions
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98
lib/colvars/colvarcomp_distances.cpp
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@ -1,3 +1,5 @@
/// -*- c++ -*-
#include <cmath>
#include "colvarmodule.h"
@ -40,6 +42,7 @@ colvar::distance::distance()
b_inverse_gradients = true;
b_Jacobian_derivative = true;
b_1site_force = false;
b_no_PBC = false;
x.type (colvarvalue::type_scalar);
}
@ -143,8 +146,9 @@ colvar::distance_z::distance_z (std::string const &conf)
b_periodic = true;
if ((wrap_center != 0.0) && (period == 0.0)) {
cvm::fatal_error ("Error: wrapAround was defined in a distanceZ component,"
" but its period has not been set.\n");
cvm::error ("Error: wrapAround was defined in a distanceZ component,"
" but its period has not been set.\n");
return;
}
parse_group (conf, "main", main);
@ -162,8 +166,10 @@ colvar::distance_z::distance_z (std::string const &conf)
cvm::log ("Warning: explicit axis definition will be ignored!");
} else {
if (get_keyval (conf, "axis", axis, cvm::rvector (0.0, 0.0, 1.0))) {
if (axis.norm2() == 0.0)
cvm::fatal_error ("Axis vector is zero!");
if (axis.norm2() == 0.0) {
cvm::error ("Axis vector is zero!");
return;
}
if (axis.norm2() != 1.0) {
axis = axis.unit();
cvm::log ("The normalized axis is: "+cvm::to_str (axis)+".\n");
@ -234,6 +240,15 @@ void colvar::distance_z::calc_gradients()
cvm::position_distance (main.center_of_mass(), ref1.center_of_mass()) + x.real_value * axis ));
}
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients for group main:\n");
debug_gradients (main);
cvm::log ("Debugging gradients for group ref1:\n");
debug_gradients (ref1);
cvm::log ("Debugging gradients for group ref2:\n");
debug_gradients (ref2);
}
}
void colvar::distance_z::calc_force_invgrads()
@ -422,16 +437,19 @@ colvar::distance_inv::distance_inv (std::string const &conf)
function_type = "distance_inv";
get_keyval (conf, "exponent", exponent, 6);
if (exponent%2) {
cvm::fatal_error ("Error: odd exponent provided, can only use even ones.\n");
cvm::error ("Error: odd exponent provided, can only use even ones.\n");
return;
}
if (exponent <= 0) {
cvm::fatal_error ("Error: negative or zero exponent provided.\n");
cvm::error ("Error: negative or zero exponent provided.\n");
return;
}
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
if (ai1->id == ai2->id)
cvm::fatal_error ("Error: group1 and group1 have some atoms in common: this is not allowed for distanceInv.\n");
cvm::error ("Error: group1 and group1 have some atoms in common: this is not allowed for distanceInv.\n");
return;
}
}
@ -640,8 +658,10 @@ colvar::inertia_z::inertia_z (std::string const &conf)
{
function_type = "inertia_z";
if (get_keyval (conf, "axis", axis, cvm::rvector (0.0, 0.0, 1.0))) {
if (axis.norm2() == 0.0)
cvm::fatal_error ("Axis vector is zero!");
if (axis.norm2() == 0.0) {
cvm::error ("Axis vector is zero!");
return;
}
if (axis.norm2() != 1.0) {
axis = axis.unit();
cvm::log ("The normalized axis is: "+cvm::to_str (axis)+".\n");
@ -700,8 +720,10 @@ colvar::rmsd::rmsd (std::string const &conf)
parse_group (conf, "atoms", atoms);
atom_groups.push_back (&atoms);
if (atoms.b_dummy)
cvm::fatal_error ("Error: \"atoms\" cannot be a dummy atom.");
if (atoms.b_dummy) {
cvm::error ("Error: \"atoms\" cannot be a dummy atom.");
return;
}
if (atoms.ref_pos_group != NULL) {
cvm::log ("The option \"refPositionsGroup\" (alternative group for fitting) was enabled: "
@ -715,10 +737,11 @@ colvar::rmsd::rmsd (std::string const &conf)
if (get_keyval (conf, "refPositions", ref_pos, ref_pos)) {
cvm::log ("Using reference positions from configuration file to calculate the variable.\n");
if (ref_pos.size() != atoms.size()) {
cvm::fatal_error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms of group \"atoms\" ("+
cvm::to_str (atoms.size())+").\n");
cvm::error ("Error: the number of reference positions provided ("+
cvm::to_str (ref_pos.size())+
") does not match the number of atoms of group \"atoms\" ("+
cvm::to_str (atoms.size())+").\n");
return;
}
}
{
@ -726,8 +749,9 @@ colvar::rmsd::rmsd (std::string const &conf)
if (get_keyval (conf, "refPositionsFile", ref_pos_file, std::string (""))) {
if (ref_pos.size()) {
cvm::fatal_error ("Error: cannot specify \"refPositionsFile\" and "
cvm::error ("Error: cannot specify \"refPositionsFile\" and "
"\"refPositions\" at the same time.\n");
return;
}
std::string ref_pos_col;
@ -737,8 +761,9 @@ colvar::rmsd::rmsd (std::string const &conf)
// if provided, use PDB column to select coordinates
bool found = get_keyval (conf, "refPositionsColValue", ref_pos_col_value, 0.0);
if (found && !ref_pos_col_value)
cvm::fatal_error ("Error: refPositionsColValue, "
cvm::error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
return;
} else {
// if not, rely on existing atom indices for the group
atoms.create_sorted_ids();
@ -897,25 +922,30 @@ colvar::eigenvector::eigenvector (std::string const &conf)
if (b_inline) {
cvm::log ("Using reference positions from input file.\n");
if (ref_pos.size() != atoms.size()) {
cvm::fatal_error ("Error: reference positions do not "
cvm::error ("Error: reference positions do not "
"match the number of requested atoms.\n");
return;
}
}
std::string file_name;
if (get_keyval (conf, "refPositionsFile", file_name)) {
if (b_inline)
cvm::fatal_error ("Error: refPositions and refPositionsFile cannot be specified at the same time.\n");
if (b_inline) {
cvm::error ("Error: refPositions and refPositionsFile cannot be specified at the same time.\n");
return;
}
std::string file_col;
double file_col_value;
if (get_keyval (conf, "refPositionsCol", file_col, std::string (""))) {
// use PDB flags if column is provided
bool found = get_keyval (conf, "refPositionsColValue", file_col_value, 0.0);
if (found && !file_col_value)
cvm::fatal_error ("Error: refPositionsColValue, "
if (found && !file_col_value) {
cvm::error ("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
return;
}
} else {
// if not, use atom indices
atoms.create_sorted_ids();
@ -965,17 +995,20 @@ colvar::eigenvector::eigenvector (std::string const &conf)
std::string file_name;
if (get_keyval (conf, "vectorFile", file_name)) {
if (b_inline)
cvm::fatal_error ("Error: vector and vectorFile cannot be specified at the same time.\n");
if (b_inline) {
cvm::error ("Error: vector and vectorFile cannot be specified at the same time.\n");
return;
}
std::string file_col;
double file_col_value;
if (get_keyval (conf, "vectorCol", file_col, std::string (""))) {
// use PDB flags if column is provided
bool found = get_keyval (conf, "vectorColValue", file_col_value, 0.0);
if (found && !file_col_value)
cvm::fatal_error ("Error: vectorColValue, "
"if provided, must be non-zero.\n");
if (found && !file_col_value) {
cvm::error ("Error: vectorColValue, if provided, must be non-zero.\n");
return;
}
} else {
// if not, use atom indices
atoms.create_sorted_ids();
@ -987,13 +1020,14 @@ colvar::eigenvector::eigenvector (std::string const &conf)
}
if (!ref_pos.size() || !eigenvec.size()) {
cvm::fatal_error ("Error: both reference coordinates"
cvm::error ("Error: both reference coordinates"
"and eigenvector must be defined.\n");
return;
}
cvm::atom_pos eig_center (0.0, 0.0, 0.0);
for (size_t i = 0; i < atoms.size(); i++) {
eig_center += eigenvec[i];
for (size_t eil = 0; eil < atoms.size(); eil++) {
eig_center += eigenvec[eil];
}
eig_center *= 1.0 / atoms.size();
cvm::log ("Geometric center of the provided vector: "+cvm::to_str (eig_center)+"\n");
@ -1038,8 +1072,8 @@ colvar::eigenvector::eigenvector (std::string const &conf)
// for inverse gradients
eigenvec_invnorm2 = 0.0;
for (size_t i = 0; i < atoms.size(); i++) {
eigenvec_invnorm2 += eigenvec[i].norm2();
for (size_t ein = 0; ein < atoms.size(); ein++) {
eigenvec_invnorm2 += eigenvec[ein].norm2();
}
eigenvec_invnorm2 = 1.0 / eigenvec_invnorm2;