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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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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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442
lib/colvars/colvar.cpp
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@ -1,33 +1,31 @@
// -*- c++ -*-
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
#include "colvarscript.h"
#include <algorithm>
// XX TODO make the acf code handle forces as well as values and velocities
colvar::colvar (std::string const &conf)
{
size_t i, j;
cvm::log ("Initializing a new collective variable.\n");
get_keyval (conf, "name", this->name,
(std::string ("colvar")+cvm::to_str (cvm::colvars.size()+1)));
for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin();
cvi < cvm::colvars.end();
cvi++) {
if ((*cvi)->name == this->name)
cvm::fatal_error ("Error: this colvar cannot have the same name, \""+this->name+
"\", as another colvar.\n");
if (cvm::colvar_by_name (this->name) != NULL) {
cvm::error ("Error: this colvar cannot have the same name, \""+this->name+
"\", as another colvar.\n",
INPUT_ERROR);
}
// all tasks disabled by default
for (size_t i = 0; i < task_ntot; i++) {
for (i = 0; i < task_ntot; i++) {
tasks[i] = false;
}
@ -57,19 +55,21 @@ colvar::colvar (std::string const &conf)
cvcp->check_keywords (def_conf, def_config_key); \
cvm::decrease_depth(); \
} else { \
cvm::fatal_error ("Error: in allocating component \"" \
def_config_key"\".\n"); \
cvm::error ("Error: in allocating component \"" \
def_config_key"\".\n", \
MEMORY_ERROR); \
} \
if ( (cvcp->period != 0.0) || (cvcp->wrap_center != 0.0) ) { \
if ( (cvcp->function_type != std::string ("distance_z")) && \
(cvcp->function_type != std::string ("dihedral")) && \
(cvcp->function_type != std::string ("spin_angle")) ) { \
cvm::fatal_error ("Error: invalid use of period and/or " \
cvm::error ("Error: invalid use of period and/or " \
"wrapAround in a \""+ \
std::string (def_config_key)+ \
"\" component.\n"+ \
"Period: "+cvm::to_str(cvcp->period) + \
" wrapAround: "+cvm::to_str(cvcp->wrap_center));\
" wrapAround: "+cvm::to_str(cvcp->wrap_center), \
INPUT_ERROR); \
} \
} \
if ( ! cvcs.back()->name.size()) \
@ -120,6 +120,8 @@ colvar::colvar (std::string const &conf)
initialize_components ("orientation", "orientation", orientation);
initialize_components ("orientation "
"angle", "orientationAngle",orientation_angle);
initialize_components ("orientation "
"projection", "orientationProj",orientation_proj);
initialize_components ("tilt", "tilt", tilt);
initialize_components ("spin angle", "spinAngle", spin_angle);
@ -135,12 +137,55 @@ colvar::colvar (std::string const &conf)
"inertiaZ", inertia_z);
initialize_components ("eigenvector", "eigenvector", eigenvector);
if (!cvcs.size())
cvm::fatal_error ("Error: no valid components were provided "
"for this collective variable.\n");
if (!cvcs.size()) {
cvm::error ("Error: no valid components were provided "
"for this collective variable.\n",
INPUT_ERROR);
}
cvm::log ("All components initialized.\n");
// Setup colvar as scripted function of components
if (get_keyval (conf, "scriptedFunction", scripted_function,
"", colvarparse::parse_silent)) {
enable(task_scripted);
cvm::log("This colvar is a scripted function.");
std::string type_str;
get_keyval (conf, "scriptedFunctionType", type_str, "scalar");
x.type(colvarvalue::type_notset);
for (i = 0; i < colvarvalue::type_all; i++) {
if (type_str == colvarvalue::type_keyword[i]) {
x.type(colvarvalue::Type(i));
break;
}
}
if (x.type() == colvarvalue::type_notset) {
cvm::error("Could not parse scripted colvar type.");
return;
}
x_reported.type (x.type());
cvm::log(std::string("Expecting colvar value of type ")
+ colvarvalue::type_desc[x.type()]);
// Build ordered list of component values that will be
// passed to the script
for (i = 1; i <= cvcs.size(); i++) {
for (j = 0; j < cvcs.size(); j++) {
if (cvcs[j]->sup_np == int(i)) {
sorted_cvc_values.push_back(cvcs[j]->p_value());
break;
}
}
}
if (sorted_cvc_values.size() != cvcs.size()) {
cvm::error("Could not find order numbers for all components"
"in componentExp values.");
return;
}
}
// this is set false if any of the components has an exponent
// different from 1 in the polynomial
@ -165,7 +210,7 @@ colvar::colvar (std::string const &conf)
}
// check the available features of each cvc
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
if ((cvcs[i])->b_debug_gradients)
enable (task_gradients);
@ -198,22 +243,26 @@ colvar::colvar (std::string const &conf)
if (! (cvcs[i])->b_Jacobian_derivative)
b_Jacobian_force = false;
for (size_t j = i; j < cvcs.size(); j++) {
if ( (cvcs[i])->type() != (cvcs[j])->type() ) {
cvm::fatal_error ("ERROR: you are definining this collective variable "
"by using components of different types, \""+
colvarvalue::type_desc[(cvcs[i])->type()]+
"\" and \""+
colvarvalue::type_desc[(cvcs[j])->type()]+
"\". "
"You must use the same type in order to "
" sum them together.\n");
if (!tasks[task_scripted]) {
// If the combination of components is a scripted function,
// the components may have different types
for (size_t j = i; j < cvcs.size(); j++) {
if ( (cvcs[i])->type() != (cvcs[j])->type() ) {
cvm::log ("ERROR: you are definining this collective variable "
"by using components of different types, \""+
colvarvalue::type_desc[(cvcs[i])->type()]+
"\" and \""+
colvarvalue::type_desc[(cvcs[j])->type()]+
"\". "
"You must use the same type in order to "
" sum them together.\n");
cvm::set_error_bits(INPUT_ERROR);
}
}
}
}
{
if (!tasks[task_scripted]) {
colvarvalue::Type const value_type = (cvcs[0])->type();
if (cvm::debug())
cvm::log ("This collective variable is a "+
@ -225,8 +274,9 @@ colvar::colvar (std::string const &conf)
}
get_keyval (conf, "width", width, 1.0);
if (width <= 0.0)
cvm::fatal_error ("Error: \"width\" must be positive.\n");
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
}
lower_boundary.type (this->type());
lower_wall.type (this->type());
@ -267,19 +317,21 @@ colvar::colvar (std::string const &conf)
// consistency checks for boundaries and walls
if (tasks[task_lower_boundary] && tasks[task_upper_boundary]) {
if (lower_boundary >= upper_boundary) {
cvm::fatal_error ("Error: the upper boundary, "+
cvm::error ("Error: the upper boundary, "+
cvm::to_str (upper_boundary)+
", is not higher than the lower boundary, "+
cvm::to_str (lower_boundary)+".\n");
cvm::to_str (lower_boundary)+".\n",
INPUT_ERROR);
}
}
if (tasks[task_lower_wall] && tasks[task_upper_wall]) {
if (lower_wall >= upper_wall) {
cvm::fatal_error ("Error: the upper wall, "+
cvm::error ("Error: the upper wall, "+
cvm::to_str (upper_wall)+
", is not higher than the lower wall, "+
cvm::to_str (lower_wall)+".\n");
cvm::to_str (lower_wall)+".\n",
INPUT_ERROR);
}
if (dist2 (lower_wall, upper_wall) < 1.0E-12) {
@ -292,14 +344,16 @@ colvar::colvar (std::string const &conf)
get_keyval (conf, "expandBoundaries", expand_boundaries, false);
if (expand_boundaries && periodic_boundaries()) {
cvm::fatal_error ("Error: trying to expand boundaries that already "
"cover a whole period of a periodic colvar.\n");
cvm::error ("Error: trying to expand boundaries that already "
"cover a whole period of a periodic colvar.\n",
INPUT_ERROR);
}
if (expand_boundaries && hard_lower_boundary && hard_upper_boundary) {
cvm::fatal_error ("Error: inconsistent configuration "
cvm::error ("Error: inconsistent configuration "
"(trying to expand boundaries with both "
"hardLowerBoundary and hardUpperBoundary enabled).\n");
}
"hardLowerBoundary and hardUpperBoundary enabled).\n",
INPUT_ERROR);
}
{
bool b_extended_lagrangian;
@ -320,21 +374,24 @@ colvar::colvar (std::string const &conf)
const bool found = get_keyval (conf, "extendedTemp", temp, cvm::temperature());
if (temp <= 0.0) {
if (found)
cvm::fatal_error ("Error: \"extendedTemp\" must be positive.\n");
cvm::log ("Error: \"extendedTemp\" must be positive.\n");
else
cvm::fatal_error ("Error: a positive temperature must be provided, either "
"by enabling a thermostat, or through \"extendedTemp\".\n");
cvm::error ("Error: a positive temperature must be provided, either "
"by enabling a thermostat, or through \"extendedTemp\".\n",
INPUT_ERROR);
}
get_keyval (conf, "extendedFluctuation", tolerance, width);
if (tolerance <= 0.0)
cvm::fatal_error ("Error: \"extendedFluctuation\" must be positive.\n");
get_keyval (conf, "extendedFluctuation", tolerance);
if (tolerance <= 0.0) {
cvm::error("Error: \"extendedFluctuation\" must be positive.\n", INPUT_ERROR);
}
ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
cvm::log ("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " kcal/mol/U^2");
get_keyval (conf, "extendedTimeConstant", period, 200.0);
if (period <= 0.0)
cvm::fatal_error ("Error: \"extendedTimeConstant\" must be positive.\n");
if (period <= 0.0) {
cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", INPUT_ERROR);
}
ext_mass = (cvm::boltzmann() * temp * period * period)
/ (4.0 * PI * PI * tolerance * tolerance);
cvm::log ("Computed fictitious mass: " + cvm::to_str(ext_mass) + " kcal/mol/(U/fs)^2 (U: colvar unit)");
@ -348,8 +405,9 @@ colvar::colvar (std::string const &conf)
}
get_keyval (conf, "extendedLangevinDamping", ext_gamma, 1.0);
if (ext_gamma < 0.0)
cvm::fatal_error ("Error: \"extendedLangevinDamping\" may not be negative.\n");
if (ext_gamma < 0.0) {
cvm::error("Error: \"extendedLangevinDamping\" may not be negative.\n", INPUT_ERROR);
}
if (ext_gamma != 0.0) {
enable (task_langevin);
ext_gamma *= 1.0e-3; // convert from ps-1 to fs-1
@ -414,7 +472,15 @@ void colvar::build_atom_list (void)
temp_id_list.sort();
temp_id_list.unique();
atom_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
// atom_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
unsigned int id_i = 0;
std::list<int>::iterator li;
for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) {
atom_ids[id_i] = *li;
id_i++;
}
temp_id_list.clear();
atomic_gradients.resize (atom_ids.size());
@ -427,7 +493,7 @@ void colvar::build_atom_list (void)
}
void colvar::parse_analysis (std::string const &conf)
int colvar::parse_analysis (std::string const &conf)
{
// if (cvm::debug())
@ -443,8 +509,9 @@ void colvar::parse_analysis (std::string const &conf)
get_keyval (conf, "runAveLength", runave_length, 1000);
get_keyval (conf, "runAveStride", runave_stride, 1);
if ((cvm::restart_out_freq % runave_stride) != 0)
cvm::fatal_error ("Error: runAveStride must be commensurate with the restart frequency.\n");
if ((cvm::restart_out_freq % runave_stride) != 0) {
cvm::error("Error: runAveStride must be commensurate with the restart frequency.\n", INPUT_ERROR);
}
std::string runave_outfile;
get_keyval (conf, "runAveOutputFile", runave_outfile,
@ -484,30 +551,33 @@ void colvar::parse_analysis (std::string const &conf)
acf_type = acf_vel;
enable (task_fdiff_velocity);
if (acf_colvar_name.size())
(cvm::colvar_p (acf_colvar_name))->enable (task_fdiff_velocity);
(cvm::colvar_by_name (acf_colvar_name))->enable (task_fdiff_velocity);
} else if (acf_type_str == to_lower_cppstr (std::string ("coordinate_p2"))) {
acf_type = acf_p2coor;
} else {
cvm::fatal_error ("Unknown type of correlation function, \""+
cvm::log ("Unknown type of correlation function, \""+
acf_type_str+"\".\n");
cvm::set_error_bits(INPUT_ERROR);
}
get_keyval (conf, "corrFuncOffset", acf_offset, 0);
get_keyval (conf, "corrFuncLength", acf_length, 1000);
get_keyval (conf, "corrFuncStride", acf_stride, 1);
if ((cvm::restart_out_freq % acf_stride) != 0)
cvm::fatal_error ("Error: corrFuncStride must be commensurate with the restart frequency.\n");
if ((cvm::restart_out_freq % acf_stride) != 0) {
cvm::error("Error: corrFuncStride must be commensurate with the restart frequency.\n", INPUT_ERROR);
}
get_keyval (conf, "corrFuncNormalize", acf_normalize, true);
get_keyval (conf, "corrFuncOutputFile", acf_outfile,
std::string (cvm::output_prefix+"."+this->name+
".corrfunc.dat"));
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void colvar::enable (colvar::task const &t)
int colvar::enable (colvar::task const &t)
{
switch (t) {
@ -528,13 +598,17 @@ void colvar::enable (colvar::task const &t)
if ( !tasks[task_extended_lagrangian] ) {
enable (task_gradients);
if (!b_Jacobian_force)
cvm::fatal_error ("Error: colvar \""+this->name+
"\" does not have Jacobian forces implemented.\n");
if (!b_linear)
cvm::fatal_error ("Error: colvar \""+this->name+
if (!b_Jacobian_force) {
cvm::error ("Error: colvar \""+this->name+
"\" does not have Jacobian forces implemented.\n",
INPUT_ERROR);
}
if (!b_linear) {
cvm::error ("Error: colvar \""+this->name+
"\" must be defined as a linear combination "
"to calculate the Jacobian force.\n");
"to calculate the Jacobian force.\n",
INPUT_ERROR);
}
if (cvm::debug())
cvm::log ("Enabling calculation of the Jacobian force "
"on this colvar.\n");
@ -545,9 +619,10 @@ void colvar::enable (colvar::task const &t)
case task_system_force:
if (!tasks[task_extended_lagrangian]) {
if (!b_inverse_gradients) {
cvm::fatal_error ("Error: one or more of the components of "
cvm::error ("Error: one or more of the components of "
"colvar \""+this->name+
"\" does not support system force calculation.\n");
"\" does not support system force calculation.\n",
INPUT_ERROR);
}
cvm::request_system_force();
}
@ -573,9 +648,11 @@ void colvar::enable (colvar::task const &t)
break;
case task_grid:
if (this->type() != colvarvalue::type_scalar)
cvm::fatal_error ("Cannot calculate a grid for collective variable, \""+
this->name+"\", because its value is not a scalar number.\n");
if (this->type() != colvarvalue::type_scalar) {
cvm::error ("Cannot calculate a grid for collective variable, \""+
this->name+"\", because its value is not a scalar number.\n",
INPUT_ERROR);
}
break;
case task_extended_lagrangian:
@ -586,8 +663,9 @@ void colvar::enable (colvar::task const &t)
case task_lower_boundary:
case task_upper_boundary:
if (this->type() != colvarvalue::type_scalar) {
cvm::fatal_error ("Error: this colvar is not a scalar value "
"and cannot produce a grid.\n");
cvm::error ("Error: this colvar is not a scalar value "
"and cannot produce a grid.\n",
INPUT_ERROR);
}
break;
@ -597,6 +675,7 @@ void colvar::enable (colvar::task const &t)
case task_ntot:
case task_langevin:
case task_output_energy:
case task_scripted:
break;
case task_gradients:
@ -605,19 +684,21 @@ void colvar::enable (colvar::task const &t)
break;
case task_collect_gradients:
if (this->type() != colvarvalue::type_scalar)
cvm::fatal_error ("Collecting atomic gradients for non-scalar collective variable \""+
this->name+"\" is not yet implemented.\n");
if (this->type() != colvarvalue::type_scalar) {
cvm::error ("Collecting atomic gradients for non-scalar collective variable \""+
this->name+"\" is not yet implemented.\n",
INPUT_ERROR);
}
enable (task_gradients);
if (atom_ids.size() == 0) {
build_atom_list();
}
break;
}
tasks[t] = true;
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -665,6 +746,7 @@ void colvar::disable (colvar::task const &t)
case task_langevin:
case task_output_energy:
case task_collect_gradients:
case task_scripted:
break;
}
@ -689,6 +771,16 @@ colvar::~colvar()
for (size_t i = 0; i < cvcs.size(); i++) {
delete cvcs[i];
}
// remove reference to this colvar from the CVM
for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin();
cvi != cvm::colvars.end();
++cvi) {
if ( *cvi == this) {
cvm::colvars.erase (cvi);
break;
}
}
}
@ -698,14 +790,15 @@ colvar::~colvar()
void colvar::calc()
{
size_t i, ig;
if (cvm::debug())
cvm::log ("Calculating colvar \""+this->name+"\".\n");
// prepare atom groups for calculation
if (cvm::debug())
cvm::log ("Collecting data from atom groups.\n");
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
atoms.reset_atoms_data();
atoms.read_positions();
@ -716,15 +809,15 @@ void colvar::calc()
}
}
if (tasks[task_output_velocity]) {
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvcs[i]->atom_groups[ig]->read_velocities();
}
}
}
if (tasks[task_system_force]) {
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvcs[i]->atom_groups[ig]->read_system_forces();
}
}
@ -735,35 +828,42 @@ void colvar::calc()
if (cvm::debug())
cvm::log ("Calculating colvar components.\n");
x.reset();
if (x.type() == colvarvalue::type_scalar) {
// polynomial combination allowed
for (size_t i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->calc_value();
cvm::decrease_depth();
if (cvm::debug())
cvm::log ("Colvar component no. "+cvm::to_str (i+1)+
" within colvar \""+this->name+"\" has value "+
cvm::to_str ((cvcs[i])->value(),
cvm::cv_width, cvm::cv_prec)+".\n");
// First, update component values
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->calc_value();
cvm::decrease_depth();
if (cvm::debug())
cvm::log ("Colvar component no. "+cvm::to_str (i+1)+
" within colvar \""+this->name+"\" has value "+
cvm::to_str ((cvcs[i])->value(),
cvm::cv_width, cvm::cv_prec)+".\n");
}
// Then combine them appropriately
if (tasks[task_scripted]) {
// cvcs combined by user script
int res = cvm::proxy->run_colvar_callback(scripted_function, sorted_cvc_values, x);
if (res == COLVARS_NOT_IMPLEMENTED) {
cvm::error("Scripted colvars are not implemented.");
return;
}
if (res != COLVARS_OK) {
cvm::error("Error running scripted colvar");
return;
}
} else if (x.type() == colvarvalue::type_scalar) {
// polynomial combination allowed
for (i = 0; i < cvcs.size(); i++) {
x += (cvcs[i])->sup_coeff *
( ((cvcs[i])->sup_np != 1) ?
std::pow ((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
(cvcs[i])->value().real_value );
( ((cvcs[i])->sup_np != 1) ?
std::pow ((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
(cvcs[i])->value().real_value );
}
} else {
// only linear combination allowed
for (size_t i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->calc_value();
cvm::decrease_depth();
if (cvm::debug())
cvm::log ("Colvar component no. "+cvm::to_str (i+1)+
" within colvar \""+this->name+"\" has value "+
cvm::to_str ((cvcs[i])->value(),
cvm::cv_width, cvm::cv_prec)+".\n");
for (i = 0; i < cvcs.size(); i++) {
x += (cvcs[i])->sup_coeff * (cvcs[i])->value();
}
}
@ -777,7 +877,7 @@ void colvar::calc()
if (cvm::debug())
cvm::log ("Calculating gradients of colvar \""+this->name+"\".\n");
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
// calculate the gradients of each component
cvm::increase_depth();
@ -785,7 +885,7 @@ void colvar::calc()
// if requested, propagate (via chain rule) the gradients above
// to the atoms used to define the roto-translation
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
if (cvcs[i]->atom_groups[ig]->b_fit_gradients)
cvcs[i]->atom_groups[ig]->calc_fit_gradients();
}
@ -797,11 +897,18 @@ void colvar::calc()
cvm::log ("Done calculating gradients of colvar \""+this->name+"\".\n");
if (tasks[task_collect_gradients]) {
if (tasks[task_scripted]) {
cvm::error("Collecting atomic gradients is not implemented for "
"scripted colvars.");
return;
}
// Collect the atomic gradients inside colvar object
for (int a = 0; a < atomic_gradients.size(); a++) {
for (unsigned int a = 0; a < atomic_gradients.size(); a++) {
atomic_gradients[a].reset();
}
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
// Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real ((cvcs[i])->sup_np) *
std::pow ((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);
@ -835,14 +942,25 @@ void colvar::calc()
if (tasks[task_system_force]) {
if (tasks[task_scripted]) {
// TODO see if this could reasonably be done in a generic way
// from generic inverse gradients
cvm::error("System force is not implemented for "
"scripted colvars.");
return;
}
if (cvm::debug())
cvm::log ("Calculating system force of colvar \""+this->name+"\".\n");
ft.reset();
if(!tasks[task_extended_lagrangian] && (cvm::step_relative() > 0)) {
// if(!tasks[task_extended_lagrangian] && (cvm::step_relative() > 0)) {
// Disabled check to allow for explicit system force calculation
// even with extended Lagrangian
if(cvm::step_relative() > 0) {
// get from the cvcs the system forces from the PREVIOUS step
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
(cvcs[i])->calc_force_invgrads();
// linear combination is assumed
cvm::increase_depth();
@ -949,15 +1067,15 @@ cvm::real colvar::update()
}
if (tasks[task_Jacobian_force]) {
size_t i;
cvm::increase_depth();
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
(cvcs[i])->calc_Jacobian_derivative();
}
cvm::decrease_depth();
fj.reset();
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
// linear combination is assumed
fj += 1.0 / ( cvm::real (cvcs.size()) * cvm::real ((cvcs[i])->sup_coeff) ) *
(cvcs[i])->Jacobian_derivative();
@ -1016,12 +1134,32 @@ cvm::real colvar::update()
void colvar::communicate_forces()
{
size_t i;
if (cvm::debug())
cvm::log ("Communicating forces from colvar \""+this->name+"\".\n");
if (x.type() == colvarvalue::type_scalar) {
if (tasks[task_scripted]) {
std::vector<colvarvalue> func_grads(cvcs.size());
int res = cvm::proxy->run_colvar_gradient_callback(scripted_function, sorted_cvc_values, func_grads);
for (size_t i = 0; i < cvcs.size(); i++) {
if (res == COLVARS_NOT_IMPLEMENTED) {
cvm::error("Colvar gradient scripts are not implemented.");
return;
}
if (res != COLVARS_OK) {
cvm::error("Error running colvar gradient script");
return;
}
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
// Note: we need a dot product here
(cvcs[i])->apply_force (f * func_grads[i]);
cvm::decrease_depth();
}
} else if (x.type() == colvarvalue::type_scalar) {
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->apply_force (f * (cvcs[i])->sup_coeff *
cvm::real ((cvcs[i])->sup_np) *
@ -1032,7 +1170,7 @@ void colvar::communicate_forces()
} else {
for (size_t i = 0; i < cvcs.size(); i++) {
for (i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->apply_force (f * (cvcs[i])->sup_coeff);
cvm::decrease_depth();
@ -1052,10 +1190,11 @@ void colvar::communicate_forces()
bool colvar::periodic_boundaries (colvarvalue const &lb, colvarvalue const &ub) const
{
if ( (!tasks[task_lower_boundary]) || (!tasks[task_upper_boundary]) ) {
cvm::fatal_error ("Error: requesting to histogram the "
cvm::log ("Error: requesting to histogram the "
"collective variable \""+this->name+"\", but a "
"pair of lower and upper boundaries must be "
"defined.\n");
cvm::set_error_bits(INPUT_ERROR);
}
if (period > 0.0) {
@ -1071,7 +1210,7 @@ bool colvar::periodic_boundaries (colvarvalue const &lb, colvarvalue const &ub)
bool colvar::periodic_boundaries() const
{
if ( (!tasks[task_lower_boundary]) || (!tasks[task_upper_boundary]) ) {
cvm::fatal_error ("Error: requesting to histogram the "
cvm::error ("Error: requesting to histogram the "
"collective variable \""+this->name+"\", but a "
"pair of lower and upper boundaries must be "
"defined.\n");
@ -1132,11 +1271,11 @@ std::istream & colvar::read_restart (std::istream &is)
if ( (get_keyval (conf, "name", check_name,
std::string (""), colvarparse::parse_silent)) &&
(check_name != name) ) {
cvm::fatal_error ("Error: the state file does not match the "
cvm::error ("Error: the state file does not match the "
"configuration file, at colvar \""+name+"\".\n");
}
if (check_name.size() == 0) {
cvm::fatal_error ("Error: Collective variable in the "
cvm::error ("Error: Collective variable in the "
"restart file without any identifier.\n");
}
}
@ -1383,7 +1522,7 @@ std::ostream & colvar::write_traj (std::ostream &os)
return os;
}
void colvar::write_output_files()
int colvar::write_output_files()
{
if (cvm::b_analysis) {
@ -1391,8 +1530,9 @@ void colvar::write_output_files()
cvm::log ("Writing acf to file \""+acf_outfile+"\".\n");
std::ofstream acf_os (acf_outfile.c_str());
if (! acf_os.good())
cvm::fatal_error ("Cannot open file \""+acf_outfile+"\".\n");
if (! acf_os.good()) {
cvm::error("Cannot open file \""+acf_outfile+"\".\n", FILE_ERROR);
}
write_acf (acf_os);
acf_os.close();
}
@ -1401,6 +1541,7 @@ void colvar::write_output_files()
runave_os.close();
}
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -1436,7 +1577,7 @@ inline void history_incr (std::list< std::list<colvarvalue> > &history
}
void colvar::calc_acf()
int colvar::calc_acf()
{
// using here an acf_stride-long list of vectors for either
// coordinates (acf_x_history) or velocities (acf_v_history); each vector can
@ -1444,17 +1585,19 @@ void colvar::calc_acf()
// representation but separated by acf_stride in the time series;
// the pointer to each vector is changed at every step
if (! (acf_x_history.size() || acf_v_history.size()) ) {
if (acf_x_history.empty() && acf_v_history.empty()) {
// first-step operations
colvar *cfcv = (acf_colvar_name.size() ?
cvm::colvar_p (acf_colvar_name) :
cvm::colvar_by_name (acf_colvar_name) :
this);
if (cfcv->type() != this->type())
cvm::fatal_error ("Error: correlation function between \""+cfcv->name+
if (cfcv->type() != this->type()) {
cvm::error ("Error: correlation function between \""+cfcv->name+
"\" and \""+this->name+"\" cannot be calculated, "
"because their value types are different.\n");
"because their value types are different.\n",
INPUT_ERROR);
}
acf_nframes = 0;
cvm::log ("Colvar \""+this->name+"\": initializing ACF calculation.\n");
@ -1462,11 +1605,12 @@ void colvar::calc_acf()
if (acf.size() < acf_length+1)
acf.resize (acf_length+1, 0.0);
size_t i;
switch (acf_type) {
case acf_vel:
// allocate space for the velocities history
for (size_t i = 0; i < acf_stride; i++) {
for (i = 0; i < acf_stride; i++) {
acf_v_history.push_back (std::list<colvarvalue>());
}
acf_v_history_p = acf_v_history.begin();
@ -1475,7 +1619,7 @@ void colvar::calc_acf()
case acf_coor:
case acf_p2coor:
// allocate space for the coordinates history
for (size_t i = 0; i < acf_stride; i++) {
for (i = 0; i < acf_stride; i++) {
acf_x_history.push_back (std::list<colvarvalue>());
}
acf_x_history_p = acf_x_history.begin();
@ -1488,7 +1632,7 @@ void colvar::calc_acf()
} else {
colvar *cfcv = (acf_colvar_name.size() ?
cvm::colvar_p (acf_colvar_name) :
cvm::colvar_by_name (acf_colvar_name) :
this);
switch (acf_type) {
@ -1532,10 +1676,11 @@ void colvar::calc_acf()
// set it for the next step
x_old = x;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
int colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
colvarvalue const &v)
{
// loop over stored velocities and add to the ACF, but only the
@ -1545,10 +1690,11 @@ void colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
vs_i++;
++vs_i;
// current vel with itself
*(acf_i++) += v.norm2();
*(acf_i) += v.norm2();
++acf_i;
// inner products of previous velocities with current (acf_i and
// vs_i are updated)
@ -1556,6 +1702,7 @@ void colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
acf_nframes++;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -1568,7 +1715,7 @@ void colvar::calc_coor_acf (std::list<colvarvalue> &x_list,
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
xs_i++;
++xs_i;
*(acf_i++) += x.norm2();
@ -1589,7 +1736,7 @@ void colvar::calc_p2coor_acf (std::list<colvarvalue> &x_list,
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
xs_i++;
++xs_i;
// value of P2(0) = 1
*(acf_i++) += 1.0;
@ -1617,7 +1764,7 @@ void colvar::write_acf (std::ostream &os)
cvm::real const acf_norm = acf.front() / cvm::real (acf_nframes);
std::vector<cvm::real>::iterator acf_i;
size_t it = acf_offset;
for (acf_i = acf.begin(); acf_i != acf.end(); acf_i++) {
for (acf_i = acf.begin(); acf_i != acf.end(); ++acf_i) {
os << std::setw (cvm::it_width) << acf_stride * (it++) << " "
<< std::setprecision (cvm::cv_prec)
<< std::setw (cvm::cv_width)
@ -1630,7 +1777,7 @@ void colvar::write_acf (std::ostream &os)
void colvar::calc_runave()
{
if (!x_history.size()) {
if (x_history.empty()) {
runave.type (x.type());
runave.reset();
@ -1653,8 +1800,9 @@ void colvar::calc_runave()
if ((*x_history_p).size() >= runave_length-1) {
runave = x;
for (std::list<colvarvalue>::iterator xs_i = (*x_history_p).begin();
xs_i != (*x_history_p).end(); xs_i++) {
std::list<colvarvalue>::iterator xs_i;
for (xs_i = (*x_history_p).begin();
xs_i != (*x_history_p).end(); ++xs_i) {
runave += (*xs_i);
}
runave *= 1.0 / cvm::real (runave_length);
@ -1662,8 +1810,8 @@ void colvar::calc_runave()
runave_variance = 0.0;
runave_variance += this->dist2 (x, runave);
for (std::list<colvarvalue>::iterator xs_i = (*x_history_p).begin();
xs_i != (*x_history_p).end(); xs_i++) {
for (xs_i = (*x_history_p).begin();
xs_i != (*x_history_p).end(); ++xs_i) {
runave_variance += this->dist2 (x, (*xs_i));
}
runave_variance *= 1.0 / cvm::real (runave_length-1);