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lammps/lib/colvars/colvar.cpp

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// -*- c++ -*-
// 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
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
#include "colvarscript.h"
// used in build_atom_list()
#include <algorithm>
/// Compare two cvcs using their names
/// Used to sort CVC array in scripted coordinates
bool compare(colvar::cvc *i, colvar::cvc *j) {
return i->name < j->name;
}
colvar::colvar()
: prev_timestep(-1)
{
// Initialize static array once and for all
runave_os = NULL;
init_cv_requires();
}
int colvar::init(std::string const &conf)
{
cvm::log("Initializing a new collective variable.\n");
colvarparse::init(conf);
int error_code = COLVARS_OK;
colvarmodule *cv = cvm::main();
get_keyval(conf, "name", this->name,
(std::string("colvar")+cvm::to_str(cv->variables()->size()+1)));
if ((cvm::colvar_by_name(this->name) != NULL) &&
(cvm::colvar_by_name(this->name) != this)) {
cvm::error("Error: this colvar cannot have the same name, \""+this->name+
"\", as another colvar.\n",
INPUT_ERROR);
return INPUT_ERROR;
}
// Initialize dependency members
// Could be a function defined in a different source file, for space?
this->description = "colvar " + this->name;
kinetic_energy = 0.0;
potential_energy = 0.0;
error_code |= init_components(conf);
if (error_code != COLVARS_OK) {
return cvm::get_error();
}
size_t i;
#ifdef LEPTON
error_code |= init_custom_function(conf);
if (error_code != COLVARS_OK) {
return cvm::get_error();
}
#endif
// Setup colvar as scripted function of components
if (get_keyval(conf, "scriptedFunction", scripted_function,
"", colvarparse::parse_silent)) {
enable(f_cv_scripted);
cvm::log("This colvar uses scripted function \"" + scripted_function + "\".");
std::string type_str;
get_keyval(conf, "scriptedFunctionType", type_str, "scalar");
x.type(colvarvalue::type_notset);
int t;
for (t = 0; t < colvarvalue::type_all; t++) {
if (type_str == colvarvalue::type_keyword(colvarvalue::Type(t))) {
x.type(colvarvalue::Type(t));
break;
}
}
if (x.type() == colvarvalue::type_notset) {
cvm::error("Could not parse scripted colvar type.", INPUT_ERROR);
return INPUT_ERROR;
}
cvm::log(std::string("Expecting colvar value of type ")
+ colvarvalue::type_desc(x.type()));
if (x.type() == colvarvalue::type_vector) {
int size;
if (!get_keyval(conf, "scriptedFunctionVectorSize", size)) {
cvm::error("Error: no size specified for vector scripted function.",
INPUT_ERROR);
return INPUT_ERROR;
}
x.vector1d_value.resize(size);
}
x_reported.type(x);
// Sort array of cvcs based on their names
// Note: default CVC names are in input order for same type of CVC
std::sort(cvcs.begin(), cvcs.end(), compare);
if(cvcs.size() > 1) {
cvm::log("Sorted list of components for this scripted colvar:");
for (i = 0; i < cvcs.size(); i++) {
cvm::log(cvm::to_str(i+1) + " " + cvcs[i]->name);
}
}
// Build ordered list of component values that will be
// passed to the script
for (i = 0; i < cvcs.size(); i++) {
sorted_cvc_values.push_back(&(cvcs[i]->value()));
}
}
if (!(is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function))) {
colvarvalue const &cvc_value = (cvcs[0])->value();
if (cvm::debug())
cvm::log ("This collective variable is a "+
colvarvalue::type_desc(cvc_value.type())+
((cvc_value.size() > 1) ? " with "+
cvm::to_str(cvc_value.size())+" individual components.\n" :
".\n"));
x.type(cvc_value);
x_reported.type(cvc_value);
}
// If using scripted biases, any colvar may receive bias forces
// and will need its gradient
if (cvm::scripted_forces()) {
enable(f_cv_gradient);
}
// check for linear combinations
{
bool lin = !(is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function));
for (i = 0; i < cvcs.size(); i++) {
// FIXME this is a reverse dependency, ie. cv feature depends on cvc flag
// need to clarify this case
// if ((cvcs[i])->b_debug_gradients)
// enable(task_gradients);
if ((cvcs[i])->sup_np != 1) {
if (cvm::debug() && lin)
cvm::log("Warning: You are using a non-linear polynomial "
"combination to define this collective variable, "
"some biasing methods may be unavailable.\n");
lin = false;
if ((cvcs[i])->sup_np < 0) {
cvm::log("Warning: you chose a negative exponent in the combination; "
"if you apply forces, the simulation may become unstable "
"when the component \""+
(cvcs[i])->function_type+"\" approaches zero.\n");
}
}
}
set_enabled(f_cv_linear, lin);
}
// Colvar is homogeneous if:
// - it is linear (hence not scripted)
// - all cvcs have coefficient 1 or -1
// i.e. sum or difference of cvcs
{
bool homogeneous = is_enabled(f_cv_linear);
for (i = 0; i < cvcs.size(); i++) {
if ((std::fabs(cvcs[i]->sup_coeff) - 1.0) > 1.0e-10) {
homogeneous = false;
}
}
set_enabled(f_cv_homogeneous, homogeneous);
}
// Colvar is deemed periodic if:
// - it is homogeneous
// - all cvcs are periodic
// - all cvcs have the same period
if (cvcs[0]->b_periodic) { // TODO make this a CVC feature
bool b_periodic = true;
period = cvcs[0]->period;
for (i = 1; i < cvcs.size(); i++) {
if (!cvcs[i]->b_periodic || cvcs[i]->period != period) {
b_periodic = false;
period = 0.0;
cvm::log("Warning: although one component is periodic, this colvar will "
"not be treated as periodic, either because the exponent is not "
"1, or because components of different periodicity are defined. "
"Make sure that you know what you are doing!");
}
}
set_enabled(f_cv_periodic, b_periodic);
}
// check that cvcs are compatible
for (i = 0; i < cvcs.size(); i++) {
// components may have different types only for scripted functions
if (!(is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function)) && (colvarvalue::check_types(cvcs[i]->value(),
cvcs[0]->value())) ) {
cvm::error("ERROR: you are definining this collective variable "
"by using components of different types. "
"You must use the same type in order to "
"sum them together.\n", INPUT_ERROR);
return INPUT_ERROR;
}
}
active_cvc_square_norm = 0.;
for (i = 0; i < cvcs.size(); i++) {
active_cvc_square_norm += cvcs[i]->sup_coeff * cvcs[i]->sup_coeff;
}
// at this point, the colvar's type is defined
f.type(value());
x_old.type(value());
v_fdiff.type(value());
v_reported.type(value());
fj.type(value());
ft.type(value());
ft_reported.type(value());
f_old.type(value());
f_old.reset();
x_restart.type(value());
after_restart = false;
reset_bias_force();
get_keyval(conf, "timeStepFactor", time_step_factor, 1);
if (time_step_factor < 0) {
cvm::error("Error: timeStepFactor must be positive.\n");
return COLVARS_ERROR;
}
if (time_step_factor != 1) {
enable(f_cv_multiple_ts);
}
// TODO use here information from the CVCs' own natural boundaries
error_code |= init_grid_parameters(conf);
error_code |= init_extended_Lagrangian(conf);
error_code |= init_output_flags(conf);
// Now that the children are defined we can solve dependencies
enable(f_cv_active);
if (cvm::b_analysis)
parse_analysis(conf);
if (cvm::debug())
cvm::log("Done initializing collective variable \""+this->name+"\".\n");
return error_code;
}
#ifdef LEPTON
int colvar::init_custom_function(std::string const &conf)
{
std::string expr;
std::vector<Lepton::ParsedExpression> pexprs;
Lepton::ParsedExpression pexpr;
size_t pos = 0; // current position in config string
double *ref;
if (!key_lookup(conf, "customFunction", &expr, &pos)) {
return COLVARS_OK;
}
enable(f_cv_custom_function);
cvm::log("This colvar uses a custom function.\n");
do {
if (cvm::debug())
cvm::log("Parsing expression \"" + expr + "\".\n");
try {
pexpr = Lepton::Parser::parse(expr);
pexprs.push_back(pexpr);
}
catch (...) {
cvm::error("Error parsing expression \"" + expr + "\".\n", INPUT_ERROR);
return INPUT_ERROR;
}
try {
value_evaluators.push_back(
new Lepton::CompiledExpression(pexpr.createCompiledExpression()));
// Define variables for cvc values
// Stored in order: expr1, cvc1, cvc2, expr2, cvc1...
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t j = 0; j < cvcs[i]->value().size(); j++) {
std::string vn = cvcs[i]->name +
(cvcs[i]->value().size() > 1 ? cvm::to_str(j+1) : "");
try {
ref =&value_evaluators.back()->getVariableReference(vn);
}
catch (...) { // Variable is absent from expression
// To keep the same workflow, we use a pointer to a double here
// that will receive CVC values - even though none was allocated by Lepton
ref = &dev_null;
if (cvm::debug())
cvm::log("Variable " + vn + " is absent from expression \"" + expr + "\".\n");
}
value_eval_var_refs.push_back(ref);
}
}
}
catch (...) {
cvm::error("Error compiling expression \"" + expr + "\".\n", INPUT_ERROR);
return INPUT_ERROR;
}
} while (key_lookup(conf, "customFunction", &expr, &pos));
// Now define derivative with respect to each scalar sub-component
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t j = 0; j < cvcs[i]->value().size(); j++) {
std::string vn = cvcs[i]->name +
(cvcs[i]->value().size() > 1 ? cvm::to_str(j+1) : "");
// Element ordering: we want the
// gradient vector of derivatives of all elements of the colvar
// wrt to a given element of a cvc ([i][j])
for (size_t c = 0; c < pexprs.size(); c++) {
gradient_evaluators.push_back(
new Lepton::CompiledExpression(pexprs[c].differentiate(vn).createCompiledExpression()));
// and record the refs to each variable in those expressions
for (size_t k = 0; k < cvcs.size(); k++) {
for (size_t l = 0; l < cvcs[k]->value().size(); l++) {
std::string vvn = cvcs[k]->name +
(cvcs[k]->value().size() > 1 ? cvm::to_str(l+1) : "");
try {
ref = &gradient_evaluators.back()->getVariableReference(vvn);
}
catch (...) { // Variable is absent from derivative
// To keep the same workflow, we use a pointer to a double here
// that will receive CVC values - even though none was allocated by Lepton
if (cvm::debug())
cvm::log("Variable " + vvn + " is absent from derivative of \"" + expr + "\" wrt " + vn + ".\n");
ref = &dev_null;
}
grad_eval_var_refs.push_back(ref);
}
}
}
}
}
if (value_evaluators.size() == 0) {
cvm::error("Error: no custom function defined.\n", INPUT_ERROR);
return INPUT_ERROR;
}
std::string type_str;
bool b_type_specified = get_keyval(conf, "customFunctionType",
type_str, "scalar", parse_silent);
x.type(colvarvalue::type_notset);
int t;
for (t = 0; t < colvarvalue::type_all; t++) {
if (type_str == colvarvalue::type_keyword(colvarvalue::Type(t))) {
x.type(colvarvalue::Type(t));
break;
}
}
if (x.type() == colvarvalue::type_notset) {
cvm::error("Could not parse custom colvar type.", INPUT_ERROR);
return INPUT_ERROR;
}
// Guess type based on number of expressions
if (!b_type_specified) {
if (value_evaluators.size() == 1) {
x.type(colvarvalue::type_scalar);
} else {
x.type(colvarvalue::type_vector);
}
}
if (x.type() == colvarvalue::type_vector) {
x.vector1d_value.resize(value_evaluators.size());
}
x_reported.type(x);
cvm::log(std::string("Expecting colvar value of type ")
+ colvarvalue::type_desc(x.type())
+ (x.type()==colvarvalue::type_vector ? " of size " + cvm::to_str(x.size()) : "")
+ ".\n");
if (x.size() != value_evaluators.size()) {
cvm::error("Error: based on custom function type, expected "
+ cvm::to_str(x.size()) + " scalar expressions, but "
+ cvm::to_str(value_evaluators.size() + " were found.\n"));
return INPUT_ERROR;
}
return COLVARS_OK;
}
#else
int colvar::init_custom_function(std::string const &conf)
{
return COLVARS_OK;
}
#endif // #ifdef LEPTON
int colvar::init_grid_parameters(std::string const &conf)
{
colvarmodule *cv = cvm::main();
get_keyval(conf, "width", width, 1.0);
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
return INPUT_ERROR;
}
lower_boundary.type(value());
upper_boundary.type(value());
upper_wall.type(value());
set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar));
if (is_enabled(f_cv_scalar)) {
if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) {
enable(f_cv_lower_boundary);
}
std::string lw_conf, uw_conf;
if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0, parse_silent)) {
cvm::log("Warning: lowerWallConstant and lowerWall are deprecated, "
"please define a harmonicWalls bias instead.\n");
lower_wall.type(value());
get_keyval(conf, "lowerWall", lower_wall, lower_boundary);
lw_conf = std::string("\n\
lowerWallConstant "+cvm::to_str(lower_wall_k*width*width)+"\n\
lowerWalls "+cvm::to_str(lower_wall)+"\n");
}
if (get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary)) {
enable(f_cv_upper_boundary);
}
if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0, parse_silent)) {
cvm::log("Warning: upperWallConstant and upperWall are deprecated, "
"please define a harmonicWalls bias instead.\n");
upper_wall.type(value());
get_keyval(conf, "upperWall", upper_wall, upper_boundary);
uw_conf = std::string("\n\
upperWallConstant "+cvm::to_str(upper_wall_k*width*width)+"\n\
upperWalls "+cvm::to_str(upper_wall)+"\n");
}
if (lw_conf.size() && uw_conf.size()) {
if (lower_wall >= 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",
INPUT_ERROR);
return INPUT_ERROR;
}
}
if (lw_conf.size() || uw_conf.size()) {
cvm::log("Generating a new harmonicWalls bias for compatibility purposes.\n");
std::string const walls_conf("\n\
harmonicWalls {\n\
name "+this->name+"w\n\
colvars "+this->name+"\n"+lw_conf+uw_conf+"\
timeStepFactor "+cvm::to_str(time_step_factor)+"\n"+
"}\n");
cv->append_new_config(walls_conf);
}
}
if (is_enabled(f_cv_lower_boundary)) {
get_keyval(conf, "hardLowerBoundary", hard_lower_boundary, false);
}
if (is_enabled(f_cv_upper_boundary)) {
get_keyval(conf, "hardUpperBoundary", hard_upper_boundary, false);
}
// consistency checks for boundaries and walls
if (is_enabled(f_cv_lower_boundary) && is_enabled(f_cv_upper_boundary)) {
if (lower_boundary >= 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",
INPUT_ERROR);
return INPUT_ERROR;
}
}
get_keyval(conf, "expandBoundaries", expand_boundaries, false);
if (expand_boundaries && periodic_boundaries()) {
cvm::error("Error: trying to expand boundaries that already "
"cover a whole period of a periodic colvar.\n",
INPUT_ERROR);
return INPUT_ERROR;
}
if (expand_boundaries && hard_lower_boundary && hard_upper_boundary) {
cvm::error("Error: inconsistent configuration "
"(trying to expand boundaries with both "
"hardLowerBoundary and hardUpperBoundary enabled).\n",
INPUT_ERROR);
return INPUT_ERROR;
}
return COLVARS_OK;
}
int colvar::init_extended_Lagrangian(std::string const &conf)
{
get_keyval_feature(this, conf, "extendedLagrangian", f_cv_extended_Lagrangian, false);
if (is_enabled(f_cv_extended_Lagrangian)) {
cvm::real temp, tolerance, period;
cvm::log("Enabling the extended Lagrangian term for colvar \""+
this->name+"\".\n");
xr.type(value());
vr.type(value());
fr.type(value());
const bool found = get_keyval(conf, "extendedTemp", temp, cvm::temperature());
if (temp <= 0.0) {
if (found)
cvm::error("Error: \"extendedTemp\" must be positive.\n", INPUT_ERROR);
else
cvm::error("Error: a positive temperature must be provided, either "
"by enabling a thermostat, or through \"extendedTemp\".\n",
INPUT_ERROR);
return INPUT_ERROR;
}
get_keyval(conf, "extendedFluctuation", tolerance);
if (tolerance <= 0.0) {
cvm::error("Error: \"extendedFluctuation\" must be positive.\n", INPUT_ERROR);
return INPUT_ERROR;
}
ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " [E]/U^2");
get_keyval(conf, "extendedTimeConstant", period, 200.0);
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) + " [E]/(U/fs)^2 (U: colvar unit)");
{
bool b_output_energy;
get_keyval(conf, "outputEnergy", b_output_energy, false);
if (b_output_energy) {
enable(f_cv_output_energy);
}
}
get_keyval(conf, "extendedLangevinDamping", ext_gamma, 1.0);
if (ext_gamma < 0.0) {
cvm::error("Error: \"extendedLangevinDamping\" may not be negative.\n", INPUT_ERROR);
return INPUT_ERROR;
}
if (ext_gamma != 0.0) {
enable(f_cv_Langevin);
ext_gamma *= 1.0e-3; // correct as long as input is required in ps-1 and cvm::dt() is in fs
// Adjust Langevin sigma for slow time step if time_step_factor != 1
ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor)));
}
}
return COLVARS_OK;
}
int colvar::init_output_flags(std::string const &conf)
{
{
bool b_output_value;
get_keyval(conf, "outputValue", b_output_value, true);
if (b_output_value) {
enable(f_cv_output_value);
}
}
{
bool b_output_velocity;
get_keyval(conf, "outputVelocity", b_output_velocity, false);
if (b_output_velocity) {
enable(f_cv_output_velocity);
}
}
{
bool temp;
if (get_keyval(conf, "outputSystemForce", temp, false, colvarparse::parse_silent)) {
cvm::error("Option outputSystemForce is deprecated: only outputTotalForce is supported instead.\n"
"The two are NOT identical: see http://colvars.github.io/totalforce.html.\n", INPUT_ERROR);
return INPUT_ERROR;
}
}
get_keyval_feature(this, conf, "outputTotalForce", f_cv_output_total_force, false);
get_keyval_feature(this, conf, "outputAppliedForce", f_cv_output_applied_force, false);
get_keyval_feature(this, conf, "subtractAppliedForce", f_cv_subtract_applied_force, false);
return COLVARS_OK;
}
// read the configuration and set up corresponding instances, for
// each type of component implemented
template<typename def_class_name> int colvar::init_components_type(std::string const &conf,
char const *def_desc,
char const *def_config_key)
{
size_t def_count = 0;
std::string def_conf = "";
size_t pos = 0;
while ( this->key_lookup(conf,
def_config_key,
&def_conf,
&pos) ) {
if (!def_conf.size()) continue;
cvm::log("Initializing "
"a new \""+std::string(def_config_key)+"\" component"+
(cvm::debug() ? ", with configuration:\n"+def_conf
: ".\n"));
cvm::increase_depth();
cvc *cvcp = new def_class_name(def_conf);
if (cvcp != NULL) {
cvcs.push_back(cvcp);
cvcp->check_keywords(def_conf, def_config_key);
if (cvm::get_error()) {
cvm::error("Error: in setting up component \""+
std::string(def_config_key)+"\".\n", INPUT_ERROR);
return INPUT_ERROR;
}
cvm::decrease_depth();
} else {
cvm::error("Error: in allocating component \""+
std::string(def_config_key)+"\".\n",
MEMORY_ERROR);
return 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("polar_phi")) &&
(cvcp->function_type != std::string("spin_angle")) ) {
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),
INPUT_ERROR);
return INPUT_ERROR;
}
}
if ( ! cvcs.back()->name.size()) {
std::ostringstream s;
s << def_config_key << std::setfill('0') << std::setw(4) << ++def_count;
cvcs.back()->name = s.str();
/* pad cvc number for correct ordering when sorting by name */
}
cvcs.back()->setup();
if (cvm::debug()) {
cvm::log("Done initializing a \""+
std::string(def_config_key)+
"\" component"+
(cvm::debug() ?
", named \""+cvcs.back()->name+"\""
: "")+".\n");
}
def_conf = "";
if (cvm::debug()) {
cvm::log("Parsed "+cvm::to_str(cvcs.size())+
" components at this time.\n");
}
}
return COLVARS_OK;
}
int colvar::init_components(std::string const &conf)
{
int error_code = COLVARS_OK;
error_code |= init_components_type<distance>(conf, "distance", "distance");
error_code |= init_components_type<distance_vec>(conf, "distance vector", "distanceVec");
error_code |= init_components_type<cartesian>(conf, "Cartesian coordinates", "cartesian");
error_code |= init_components_type<distance_dir>(conf, "distance vector "
"direction", "distanceDir");
error_code |= init_components_type<distance_z>(conf, "distance projection "
"on an axis", "distanceZ");
error_code |= init_components_type<distance_xy>(conf, "distance projection "
"on a plane", "distanceXY");
error_code |= init_components_type<polar_theta>(conf, "spherical polar angle theta",
"polarTheta");
error_code |= init_components_type<polar_phi>(conf, "spherical azimuthal angle phi",
"polarPhi");
error_code |= init_components_type<distance_inv>(conf, "average distance "
"weighted by inverse power", "distanceInv");
error_code |= init_components_type<distance_pairs>(conf, "N1xN2-long vector "
"of pairwise distances", "distancePairs");
error_code |= init_components_type<coordnum>(conf, "coordination "
"number", "coordNum");
error_code |= init_components_type<selfcoordnum>(conf, "self-coordination "
"number", "selfCoordNum");
error_code |= init_components_type<groupcoordnum>(conf, "group-coordination "
"number", "groupCoord");
error_code |= init_components_type<angle>(conf, "angle", "angle");
error_code |= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle");
error_code |= init_components_type<dihedral>(conf, "dihedral", "dihedral");
error_code |= init_components_type<h_bond>(conf, "hydrogen bond", "hBond");
error_code |= init_components_type<alpha_angles>(conf, "alpha helix", "alpha");
error_code |= init_components_type<dihedPC>(conf, "dihedral "
"principal component", "dihedralPC");
error_code |= init_components_type<orientation>(conf, "orientation", "orientation");
error_code |= init_components_type<orientation_angle>(conf, "orientation "
"angle", "orientationAngle");
error_code |= init_components_type<orientation_proj>(conf, "orientation "
"projection", "orientationProj");
error_code |= init_components_type<tilt>(conf, "tilt", "tilt");
error_code |= init_components_type<spin_angle>(conf, "spin angle", "spinAngle");
error_code |= init_components_type<rmsd>(conf, "RMSD", "rmsd");
error_code |= init_components_type<gyration>(conf, "radius of "
"gyration", "gyration");
error_code |= init_components_type<inertia>(conf, "moment of "
"inertia", "inertia");
error_code |= init_components_type<inertia_z>(conf, "moment of inertia around an axis", "inertiaZ");
error_code |= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");
if (!cvcs.size() || (error_code != COLVARS_OK)) {
cvm::error("Error: no valid components were provided "
"for this collective variable.\n",
INPUT_ERROR);
return INPUT_ERROR;
}
n_active_cvcs = cvcs.size();
cvm::log("All components initialized.\n");
// Store list of children cvcs for dependency checking purposes
for (size_t i = 0; i < cvcs.size(); i++) {
add_child(cvcs[i]);
}
return COLVARS_OK;
}
void colvar::do_feature_side_effects(int id)
{
switch (id) {
case f_cv_total_force_calc:
cvm::request_total_force();
break;
case f_cv_collect_gradient:
if (atom_ids.size() == 0) {
build_atom_list();
}
break;
}
}
void colvar::build_atom_list(void)
{
// If atomic gradients are requested, build full list of atom ids from all cvcs
std::list<int> temp_id_list;
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) {
cvm::atom_group &ag = *(cvcs[i]->atom_groups[j]);
for (size_t k = 0; k < ag.size(); k++) {
temp_id_list.push_back(ag[k].id);
}
}
}
temp_id_list.sort();
temp_id_list.unique();
// 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());
if (atom_ids.size()) {
if (cvm::debug())
cvm::log("Colvar: created atom list with " + cvm::to_str(atom_ids.size()) + " atoms.\n");
} else {
cvm::log("Warning: colvar components communicated no atom IDs.\n");
}
}
int colvar::parse_analysis(std::string const &conf)
{
// if (cvm::debug())
// cvm::log ("Parsing analysis flags for collective variable \""+
// this->name+"\".\n");
runave_length = 0;
bool b_runave = false;
if (get_keyval(conf, "runAve", b_runave) && b_runave) {
enable(f_cv_runave);
get_keyval(conf, "runAveLength", runave_length, 1000);
get_keyval(conf, "runAveStride", runave_stride, 1);
if ((cvm::restart_out_freq % runave_stride) != 0) {
cvm::error("Error: runAveStride must be commensurate with the restart frequency.\n", INPUT_ERROR);
}
get_keyval(conf, "runAveOutputFile", runave_outfile,
std::string(cvm::output_prefix()+"."+
this->name+".runave.traj"));
size_t const this_cv_width = x.output_width(cvm::cv_width);
cvm::proxy->backup_file(runave_outfile);
runave_os = cvm::proxy->output_stream(runave_outfile);
*runave_os << "# " << cvm::wrap_string("step", cvm::it_width-2)
<< " "
<< cvm::wrap_string("running average", this_cv_width)
<< " "
<< cvm::wrap_string("running stddev", this_cv_width)
<< "\n";
}
acf_length = 0;
bool b_acf = false;
if (get_keyval(conf, "corrFunc", b_acf) && b_acf) {
enable(f_cv_corrfunc);
std::string acf_colvar_name;
get_keyval(conf, "corrFuncWithColvar", acf_colvar_name, this->name);
if (acf_colvar_name == this->name) {
cvm::log("Calculating auto-correlation function.\n");
} else {
cvm::log("Calculating correlation function with \""+
this->name+"\".\n");
}
std::string acf_type_str;
get_keyval(conf, "corrFuncType", acf_type_str, to_lower_cppstr(std::string("velocity")));
if (acf_type_str == to_lower_cppstr(std::string("coordinate"))) {
acf_type = acf_coor;
} else if (acf_type_str == to_lower_cppstr(std::string("velocity"))) {
acf_type = acf_vel;
enable(f_cv_fdiff_velocity);
if (acf_colvar_name.size())
(cvm::colvar_by_name(acf_colvar_name))->enable(f_cv_fdiff_velocity);
} else if (acf_type_str == to_lower_cppstr(std::string("coordinate_p2"))) {
acf_type = acf_p2coor;
} else {
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::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::setup() {
// loop over all components to reset masses of all groups
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
atoms.setup();
atoms.reset_mass(name,i,ig);
atoms.read_positions();
}
}
}
colvar::~colvar()
{
// There is no need to call free_children_deps() here
// because the children are cvcs and will be deleted
// just below
// Clear references to this colvar's cvcs as children
// for dependency purposes
remove_all_children();
for (std::vector<cvc *>::reverse_iterator ci = cvcs.rbegin();
ci != cvcs.rend();
++ci) {
// clear all children of this cvc (i.e. its atom groups)
// because the cvc base class destructor can't do it early enough
// and we don't want to have each cvc derived class do it separately
(*ci)->remove_all_children();
delete *ci;
}
// remove reference to this colvar from the CVM
colvarmodule *cv = cvm::main();
for (std::vector<colvar *>::iterator cvi = cv->variables()->begin();
cvi != cv->variables()->end();
++cvi) {
if ( *cvi == this) {
cv->variables()->erase(cvi);
break;
}
}
#ifdef LEPTON
for (std::vector<Lepton::CompiledExpression *>::iterator cei = value_evaluators.begin();
cei != value_evaluators.end();
++cei) {
if (*cei != NULL) delete (*cei);
}
value_evaluators.clear();
for (std::vector<Lepton::CompiledExpression *>::iterator gei = gradient_evaluators.begin();
gei != gradient_evaluators.end();
++gei) {
if (*gei != NULL) delete (*gei);
}
gradient_evaluators.clear();
#endif
}
// ******************** CALC FUNCTIONS ********************
// Default schedule (everything is serialized)
int colvar::calc()
{
// Note: if anything is added here, it should be added also in the SMP block of calc_colvars()
int error_code = COLVARS_OK;
if (is_enabled(f_cv_active)) {
error_code |= update_cvc_flags();
if (error_code != COLVARS_OK) return error_code;
error_code |= calc_cvcs();
if (error_code != COLVARS_OK) return error_code;
error_code |= collect_cvc_data();
}
return error_code;
}
int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
{
colvarproxy *proxy = cvm::main()->proxy;
int error_code = COLVARS_OK;
if (cvm::debug())
cvm::log("Calculating colvar \""+this->name+"\", components "+
cvm::to_str(first_cvc)+" through "+cvm::to_str(first_cvc+num_cvcs)+".\n");
error_code |= check_cvc_range(first_cvc, num_cvcs);
if (error_code != COLVARS_OK) {
return error_code;
}
if ((cvm::step_relative() > 0) && (!proxy->total_forces_same_step())){
// Use Jacobian derivative from previous timestep
error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
}
// atom coordinates are updated by the next line
error_code |= calc_cvc_values(first_cvc, num_cvcs);
error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
if (proxy->total_forces_same_step()){
// Use Jacobian derivative from this timestep
error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
}
if (cvm::debug())
cvm::log("Done calculating colvar \""+this->name+"\".\n");
return error_code;
}
int colvar::collect_cvc_data()
{
if (cvm::debug())
cvm::log("Calculating colvar \""+this->name+"\"'s properties.\n");
int error_code = COLVARS_OK;
if (cvm::step_relative() > 0) {
// Total force depends on Jacobian derivative from previous timestep
// collect_cvc_total_forces() uses the previous value of jd
error_code |= collect_cvc_total_forces();
}
error_code |= collect_cvc_values();
error_code |= collect_cvc_gradients();
error_code |= collect_cvc_Jacobians();
error_code |= calc_colvar_properties();
if (cvm::debug())
cvm::log("Done calculating colvar \""+this->name+"\"'s properties.\n");
return error_code;
}
int colvar::check_cvc_range(int first_cvc, size_t num_cvcs)
{
if ((first_cvc < 0) || (first_cvc >= ((int) cvcs.size()))) {
cvm::error("Error: trying to address a component outside the "
"range defined for colvar \""+name+"\".\n", BUG_ERROR);
return BUG_ERROR;
}
return COLVARS_OK;
}
int colvar::calc_cvc_values(int first_cvc, size_t num_cvcs)
{
size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
size_t i, cvc_count;
// calculate the value of the colvar
if (cvm::debug())
cvm::log("Calculating colvar components.\n");
// First, calculate component values
cvm::increase_depth();
for (i = first_cvc, cvc_count = 0;
(i < cvcs.size()) && (cvc_count < cvc_max_count);
i++) {
if (!cvcs[i]->is_enabled()) continue;
cvc_count++;
(cvcs[i])->read_data();
(cvcs[i])->calc_value();
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");
}
cvm::decrease_depth();
return COLVARS_OK;
}
int colvar::collect_cvc_values()
{
x.reset();
// combine them appropriately, using either a scripted function or a polynomial
if (is_enabled(f_cv_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 COLVARS_NOT_IMPLEMENTED;
}
if (res != COLVARS_OK) {
cvm::error("Error running scripted colvar");
return COLVARS_OK;
}
#ifdef LEPTON
} else if (is_enabled(f_cv_custom_function)) {
size_t l = 0; // index in the vector of variable references
for (size_t i = 0; i < x.size(); i++) {
// Fill Lepton evaluator variables with CVC values, serialized into scalars
for (size_t j = 0; j < cvcs.size(); j++) {
for (size_t k = 0; k < cvcs[j]->value().size(); k++) {
*(value_eval_var_refs[l++]) = cvcs[j]->value()[k];
}
}
x[i] = value_evaluators[i]->evaluate();
}
#endif
} else if (x.type() == colvarvalue::type_scalar) {
// polynomial combination allowed
for (size_t i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
x += (cvcs[i])->sup_coeff *
( ((cvcs[i])->sup_np != 1) ?
cvm::integer_power((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
(cvcs[i])->value().real_value );
}
} else {
for (size_t i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
x += (cvcs[i])->sup_coeff * (cvcs[i])->value();
}
}
if (cvm::debug())
cvm::log("Colvar \""+this->name+"\" has value "+
cvm::to_str(x, cvm::cv_width, cvm::cv_prec)+".\n");
if (after_restart) {
if (cvm::proxy->simulation_running()) {
cvm::real const jump2 = dist2(x, x_restart) / (width*width);
if (jump2 > 0.25) {
cvm::error("Error: the calculated value of colvar \""+name+
"\":\n"+cvm::to_str(x)+"\n differs greatly from the value "
"last read from the state file:\n"+cvm::to_str(x_restart)+
"\nPossible causes are changes in configuration, "
"wrong state file, or how PBC wrapping is handled.\n",
INPUT_ERROR);
return INPUT_ERROR;
}
}
}
return COLVARS_OK;
}
int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs)
{
size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
size_t i, cvc_count;
if (cvm::debug())
cvm::log("Calculating gradients of colvar \""+this->name+"\".\n");
// calculate the gradients of each component
cvm::increase_depth();
for (i = first_cvc, cvc_count = 0;
(i < cvcs.size()) && (cvc_count < cvc_max_count);
i++) {
if (!cvcs[i]->is_enabled()) continue;
cvc_count++;
if ((cvcs[i])->is_enabled(f_cvc_gradient)) {
(cvcs[i])->calc_gradients();
// if requested, propagate (via chain rule) the gradients above
// to the atoms used to define the roto-translation
(cvcs[i])->calc_fit_gradients();
if ((cvcs[i])->is_enabled(f_cvc_debug_gradient))
(cvcs[i])->debug_gradients();
}
cvm::decrease_depth();
if (cvm::debug())
cvm::log("Done calculating gradients of colvar \""+this->name+"\".\n");
}
return COLVARS_OK;
}
int colvar::collect_cvc_gradients()
{
size_t i;
if (is_enabled(f_cv_collect_gradient)) {
// Collect the atomic gradients inside colvar object
for (unsigned int a = 0; a < atomic_gradients.size(); a++) {
atomic_gradients[a].reset();
}
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
// Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real((cvcs[i])->sup_np) *
cvm::integer_power((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);
for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) {
cvm::atom_group &ag = *(cvcs[i]->atom_groups[j]);
// If necessary, apply inverse rotation to get atomic
// gradient in the laboratory frame
if (ag.b_rotate) {
cvm::rotation const rot_inv = ag.rot.inverse();
for (size_t k = 0; k < ag.size(); k++) {
size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
ag[k].id) - atom_ids.begin();
atomic_gradients[a] += coeff * rot_inv.rotate(ag[k].grad);
}
} else {
for (size_t k = 0; k < ag.size(); k++) {
size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
ag[k].id) - atom_ids.begin();
atomic_gradients[a] += coeff * ag[k].grad;
}
}
}
}
}
return COLVARS_OK;
}
int colvar::calc_cvc_total_force(int first_cvc, size_t num_cvcs)
{
size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
size_t i, cvc_count;
if (is_enabled(f_cv_total_force_calc)) {
if (cvm::debug())
cvm::log("Calculating total force of colvar \""+this->name+"\".\n");
cvm::increase_depth();
for (i = first_cvc, cvc_count = 0;
(i < cvcs.size()) && (cvc_count < cvc_max_count);
i++) {
if (!cvcs[i]->is_enabled()) continue;
cvc_count++;
(cvcs[i])->calc_force_invgrads();
}
cvm::decrease_depth();
if (cvm::debug())
cvm::log("Done calculating total force of colvar \""+this->name+"\".\n");
}
return COLVARS_OK;
}
int colvar::collect_cvc_total_forces()
{
if (is_enabled(f_cv_total_force_calc)) {
ft.reset();
if (cvm::step_relative() > 0) {
// get from the cvcs the total forces from the PREVIOUS step
for (size_t i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
if (cvm::debug())
cvm::log("Colvar component no. "+cvm::to_str(i+1)+
" within colvar \""+this->name+"\" has total force "+
cvm::to_str((cvcs[i])->total_force(),
cvm::cv_width, cvm::cv_prec)+".\n");
// linear combination is assumed
ft += (cvcs[i])->total_force() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
}
}
if (!is_enabled(f_cv_hide_Jacobian)) {
// add the Jacobian force to the total force, and don't apply any silent
// correction internally: biases such as colvarbias_abf will handle it
ft += fj;
}
}
return COLVARS_OK;
}
int colvar::calc_cvc_Jacobians(int first_cvc, size_t num_cvcs)
{
size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
if (is_enabled(f_cv_Jacobian)) {
cvm::increase_depth();
size_t i, cvc_count;
for (i = first_cvc, cvc_count = 0;
(i < cvcs.size()) && (cvc_count < cvc_max_count);
i++) {
if (!cvcs[i]->is_enabled()) continue;
cvc_count++;
(cvcs[i])->calc_Jacobian_derivative();
}
cvm::decrease_depth();
}
return COLVARS_OK;
}
int colvar::collect_cvc_Jacobians()
{
if (is_enabled(f_cv_Jacobian)) {
fj.reset();
for (size_t i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
if (cvm::debug())
cvm::log("Colvar component no. "+cvm::to_str(i+1)+
" within colvar \""+this->name+"\" has Jacobian derivative"+
cvm::to_str((cvcs[i])->Jacobian_derivative(),
cvm::cv_width, cvm::cv_prec)+".\n");
// linear combination is assumed
fj += (cvcs[i])->Jacobian_derivative() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
}
fj *= cvm::boltzmann() * cvm::temperature();
}
return COLVARS_OK;
}
int colvar::calc_colvar_properties()
{
if (is_enabled(f_cv_fdiff_velocity)) {
// calculate the velocity by finite differences
if (cvm::step_relative() == 0)
x_old = x;
else {
v_fdiff = fdiff_velocity(x_old, x);
v_reported = v_fdiff;
}
}
if (is_enabled(f_cv_extended_Lagrangian)) {
// initialize the restraint center in the first step to the value
// just calculated from the cvcs
if (cvm::step_relative() == 0 && !after_restart) {
xr = x;
vr.reset(); // (already 0; added for clarity)
}
// report the restraint center as "value"
x_reported = xr;
v_reported = vr;
// the "total force" with the extended Lagrangian is
// calculated in update_forces_energy() below
} else {
if (is_enabled(f_cv_subtract_applied_force)) {
// correct the total force only if it has been measured
// TODO add a specific test instead of relying on sq norm
if (ft.norm2() > 0.0) {
ft -= f_old;
}
}
x_reported = x;
ft_reported = ft;
}
// At the end of the first update after a restart, we can reset the flag
after_restart = false;
return COLVARS_OK;
}
cvm::real colvar::update_forces_energy()
{
if (cvm::debug())
cvm::log("Updating colvar \""+this->name+"\".\n");
// set to zero the applied force
f.type(value());
f.reset();
fr.reset();
// If we are not active at this timestep, that's all we have to do
// return with energy == zero
if (!is_enabled(f_cv_active)) return 0.;
// add the biases' force, which at this point should already have
// been summed over each bias using this colvar
f += fb;
if (is_enabled(f_cv_Jacobian)) {
// the instantaneous Jacobian force was not included in the reported total force;
// instead, it is subtracted from the applied force (silent Jacobian correction)
// This requires the Jacobian term for the *current* timestep
if (is_enabled(f_cv_hide_Jacobian))
f -= fj;
}
// At this point f is the force f from external biases that will be applied to the
// extended variable if there is one
if (is_enabled(f_cv_extended_Lagrangian)) {
if (cvm::debug()) {
cvm::log("Updating extended-Lagrangian degree of freedom.\n");
}
if (prev_timestep > -1) {
// Keep track of slow timestep to integrate MTS colvars
// the colvar checks the interval after waking up twice
int n_timesteps = cvm::step_relative() - prev_timestep;
if (n_timesteps != 0 && n_timesteps != time_step_factor) {
cvm::error("Error: extended-Lagrangian " + description + " has timeStepFactor " +
cvm::to_str(time_step_factor) + ", but was activated after " + cvm::to_str(n_timesteps) +
" steps at timestep " + cvm::to_str(cvm::step_absolute()) + " (relative step: " +
cvm::to_str(cvm::step_relative()) + ").\n" +
"Make sure that this colvar is requested by biases at multiples of timeStepFactor.\n");
return 0.;
}
}
prev_timestep = cvm::step_relative();
// Integrate with slow timestep (if time_step_factor != 1)
cvm::real dt = cvm::dt() * cvm::real(time_step_factor);
colvarvalue f_ext(fr.type()); // force acting on the extended variable
f_ext.reset();
// the total force is applied to the fictitious mass, while the
// atoms only feel the harmonic force + wall force
// fr: bias force on extended variable (without harmonic spring), for output in trajectory
// f_ext: total force on extended variable (including harmonic spring)
// f: - initially, external biasing force
// - after this code block, colvar force to be applied to atomic coordinates
// ie. spring force (fb_actual will be added just below)
fr = f;
// External force has been scaled for a 1-timestep impulse, scale it back because we will
// integrate it with the colvar's own timestep factor
f_ext = f / cvm::real(time_step_factor);
f_ext += (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
// Coupling force is a slow force, to be applied to atomic coords impulse-style
f *= cvm::real(time_step_factor);
if (is_enabled(f_cv_subtract_applied_force)) {
// Report a "system" force without the biases on this colvar
// that is, just the spring force
ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
} else {
// The total force acting on the extended variable is f_ext
// This will be used in the next timestep
ft_reported = f_ext;
}
// leapfrog: starting from x_i, f_i, v_(i-1/2)
vr += (0.5 * dt) * f_ext / ext_mass;
// Because of leapfrog, kinetic energy at time i is approximate
kinetic_energy = 0.5 * ext_mass * vr * vr;
potential_energy = 0.5 * ext_force_k * this->dist2(xr, x);
// leap to v_(i+1/2)
if (is_enabled(f_cv_Langevin)) {
vr -= dt * ext_gamma * vr;
colvarvalue rnd(x);
rnd.set_random();
vr += dt * ext_sigma * rnd / ext_mass;
}
vr += (0.5 * dt) * f_ext / ext_mass;
xr += dt * vr;
xr.apply_constraints();
if (this->is_enabled(f_cv_periodic)) this->wrap(xr);
}
// Now adding the force on the actual colvar (for those biases that
// bypass the extended Lagrangian mass)
f += fb_actual;
if (is_enabled(f_cv_fdiff_velocity)) {
// set it for the next step
x_old = x;
}
if (is_enabled(f_cv_subtract_applied_force)) {
f_old = f;
}
if (cvm::debug())
cvm::log("Done updating colvar \""+this->name+"\".\n");
return (potential_energy + kinetic_energy);
}
void colvar::communicate_forces()
{
size_t i;
if (cvm::debug()) {
cvm::log("Communicating forces from colvar \""+this->name+"\".\n");
cvm::log("Force to be applied: " + cvm::to_str(f) + "\n");
}
if (is_enabled(f_cv_scripted)) {
std::vector<cvm::matrix2d<cvm::real> > func_grads;
func_grads.reserve(cvcs.size());
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
func_grads.push_back(cvm::matrix2d<cvm::real> (x.size(),
cvcs[i]->value().size()));
}
int res = cvm::proxy->run_colvar_gradient_callback(scripted_function, sorted_cvc_values, func_grads);
if (res != COLVARS_OK) {
if (res == COLVARS_NOT_IMPLEMENTED) {
cvm::error("Colvar gradient scripts are not implemented.", COLVARS_NOT_IMPLEMENTED);
} else {
cvm::error("Error running colvar gradient script");
}
return;
}
int grad_index = 0; // index in the scripted gradients, to account for some components being disabled
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
// cvc force is colvar force times colvar/cvc Jacobian
// (vector-matrix product)
(cvcs[i])->apply_force(colvarvalue(f.as_vector() * func_grads[grad_index++],
cvcs[i]->value().type()));
}
#ifdef LEPTON
} else if (is_enabled(f_cv_custom_function)) {
size_t r = 0; // index in the vector of variable references
size_t e = 0; // index of the gradient evaluator
for (size_t i = 0; i < cvcs.size(); i++) { // gradient with respect to cvc i
cvm::matrix2d<cvm::real> jacobian (x.size(), cvcs[i]->value().size());
for (size_t j = 0; j < cvcs[i]->value().size(); j++) { // j-th element
for (size_t c = 0; c < x.size(); c++) { // derivative of scalar element c of the colvarvalue
// Feed cvc values to the evaluator
for (size_t k = 0; k < cvcs.size(); k++) { //
for (size_t l = 0; l < cvcs[k]->value().size(); l++) {
*(grad_eval_var_refs[r++]) = cvcs[k]->value()[l];
}
}
jacobian[c][j] = gradient_evaluators[e++]->evaluate();
}
}
// cvc force is colvar force times colvar/cvc Jacobian
// (vector-matrix product)
(cvcs[i])->apply_force(colvarvalue(f.as_vector() * jacobian,
cvcs[i]->value().type()));
}
#endif
} else if (x.type() == colvarvalue::type_scalar) {
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
(cvcs[i])->apply_force(f * (cvcs[i])->sup_coeff *
cvm::real((cvcs[i])->sup_np) *
(cvm::integer_power((cvcs[i])->value().real_value,
(cvcs[i])->sup_np-1)) );
}
} else {
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
(cvcs[i])->apply_force(f * (cvcs[i])->sup_coeff);
}
}
if (cvm::debug())
cvm::log("Done communicating forces from colvar \""+this->name+"\".\n");
}
int colvar::set_cvc_flags(std::vector<bool> const &flags)
{
if (flags.size() != cvcs.size()) {
cvm::error("ERROR: Wrong number of CVC flags provided.");
return COLVARS_ERROR;
}
// We cannot enable or disable cvcs in the middle of a timestep or colvar evaluation sequence
// so we store the flags that will be enforced at the next call to calc()
cvc_flags = flags;
return COLVARS_OK;
}
int colvar::update_cvc_flags()
{
// Update the enabled/disabled status of cvcs if necessary
if (cvc_flags.size()) {
n_active_cvcs = 0;
active_cvc_square_norm = 0.;
for (size_t i = 0; i < cvcs.size(); i++) {
cvcs[i]->set_enabled(f_cvc_active, cvc_flags[i]);
if (cvcs[i]->is_enabled()) {
n_active_cvcs++;
active_cvc_square_norm += cvcs[i]->sup_coeff * cvcs[i]->sup_coeff;
}
}
if (!n_active_cvcs) {
cvm::error("ERROR: All CVCs are disabled for colvar " + this->name +"\n");
return COLVARS_ERROR;
}
cvc_flags.clear();
}
return COLVARS_OK;
}
// ******************** METRIC FUNCTIONS ********************
// Use the metrics defined by \link cvc \endlink objects
bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) const
{
if ( (!is_enabled(f_cv_lower_boundary)) || (!is_enabled(f_cv_upper_boundary)) ) {
cvm::log("Error: checking periodicity for collective variable \""+this->name+"\" "
"requires lower and upper boundaries to be defined.\n");
cvm::set_error_bits(INPUT_ERROR);
}
if (period > 0.0) {
if ( ((std::sqrt(this->dist2(lb, ub))) / this->width)
< 1.0E-10 ) {
return true;
}
}
return false;
}
bool colvar::periodic_boundaries() const
{
if ( (!is_enabled(f_cv_lower_boundary)) || (!is_enabled(f_cv_upper_boundary)) ) {
cvm::log("Error: checking periodicity for collective variable \""+this->name+"\" "
"requires lower and upper boundaries to be defined.\n");
}
return periodic_boundaries(lower_boundary, upper_boundary);
}
cvm::real colvar::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
if (is_enabled(f_cv_homogeneous)) {
return (cvcs[0])->dist2(x1, x2);
} else {
return x1.dist2(x2);
}
}
colvarvalue colvar::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
if (is_enabled(f_cv_homogeneous)) {
return (cvcs[0])->dist2_lgrad(x1, x2);
} else {
return x1.dist2_grad(x2);
}
}
colvarvalue colvar::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
if (is_enabled(f_cv_homogeneous)) {
return (cvcs[0])->dist2_rgrad(x1, x2);
} else {
return x2.dist2_grad(x1);
}
}
void colvar::wrap(colvarvalue &x) const
{
if (is_enabled(f_cv_homogeneous)) {
(cvcs[0])->wrap(x);
}
return;
}
// ******************** INPUT FUNCTIONS ********************
std::istream & colvar::read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string conf;
if ( !(is >> colvarparse::read_block("colvar", conf)) ) {
// this is not a colvar block
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
{
std::string check_name = "";
if ( (get_keyval(conf, "name", check_name,
std::string(""), colvarparse::parse_silent)) &&
(check_name != name) ) {
cvm::error("Error: the state file does not match the "
"configuration file, at colvar \""+name+"\".\n");
}
if (check_name.size() == 0) {
cvm::error("Error: Collective variable in the "
"restart file without any identifier.\n");
}
}
if ( !(get_keyval(conf, "x", x, x, colvarparse::parse_silent)) ) {
cvm::log("Error: restart file does not contain "
"the value of the colvar \""+
name+"\" .\n");
} else {
cvm::log("Restarting collective variable \""+name+"\" from value: "+
cvm::to_str(x)+"\n");
x_restart = x;
after_restart = true;
}
if (is_enabled(f_cv_extended_Lagrangian)) {
if ( !(get_keyval(conf, "extended_x", xr,
colvarvalue(x.type()), colvarparse::parse_silent)) &&
!(get_keyval(conf, "extended_v", vr,
colvarvalue(x.type()), colvarparse::parse_silent)) ) {
cvm::log("Error: restart file does not contain "
"\"extended_x\" or \"extended_v\" for the colvar \""+
name+"\", but you requested \"extendedLagrangian\".\n");
}
x_reported = xr;
} else {
x_reported = x;
}
if (is_enabled(f_cv_output_velocity)) {
if ( !(get_keyval(conf, "v", v_fdiff,
colvarvalue(x.type()), colvarparse::parse_silent)) ) {
cvm::log("Error: restart file does not contain "
"the velocity for the colvar \""+
name+"\", but you requested \"outputVelocity\".\n");
}
if (is_enabled(f_cv_extended_Lagrangian)) {
v_reported = vr;
} else {
v_reported = v_fdiff;
}
}
return is;
}
std::istream & colvar::read_traj(std::istream &is)
{
size_t const start_pos = is.tellg();
if (is_enabled(f_cv_output_value)) {
if (!(is >> x)) {
cvm::log("Error: in reading the value of colvar \""+
this->name+"\" from trajectory.\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
if (is_enabled(f_cv_extended_Lagrangian)) {
is >> xr;
x_reported = xr;
} else {
x_reported = x;
}
}
if (is_enabled(f_cv_output_velocity)) {
is >> v_fdiff;
if (is_enabled(f_cv_extended_Lagrangian)) {
is >> vr;
v_reported = vr;
} else {
v_reported = v_fdiff;
}
}
if (is_enabled(f_cv_output_total_force)) {
is >> ft;
ft_reported = ft;
}
if (is_enabled(f_cv_output_applied_force)) {
is >> f;
}
return is;
}
// ******************** OUTPUT FUNCTIONS ********************
std::ostream & colvar::write_restart(std::ostream &os) {
os << "colvar {\n"
<< " name " << name << "\n"
<< " x "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< x << "\n";
if (is_enabled(f_cv_output_velocity)) {
os << " v "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< v_reported << "\n";
}
if (is_enabled(f_cv_extended_Lagrangian)) {
os << " extended_x "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< xr << "\n"
<< " extended_v "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< vr << "\n";
}
os << "}\n\n";
return os;
}
std::ostream & colvar::write_traj_label(std::ostream & os)
{
size_t const this_cv_width = x.output_width(cvm::cv_width);
os << " ";
if (is_enabled(f_cv_output_value)) {
os << " "
<< cvm::wrap_string(this->name, this_cv_width);
if (is_enabled(f_cv_extended_Lagrangian)) {
// extended DOF
os << " r_"
<< cvm::wrap_string(this->name, this_cv_width-2);
}
}
if (is_enabled(f_cv_output_velocity)) {
os << " v_"
<< cvm::wrap_string(this->name, this_cv_width-2);
if (is_enabled(f_cv_extended_Lagrangian)) {
// extended DOF
os << " vr_"
<< cvm::wrap_string(this->name, this_cv_width-3);
}
}
if (is_enabled(f_cv_output_energy)) {
os << " Ep_"
<< cvm::wrap_string(this->name, this_cv_width-3)
<< " Ek_"
<< cvm::wrap_string(this->name, this_cv_width-3);
}
if (is_enabled(f_cv_output_total_force)) {
os << " ft_"
<< cvm::wrap_string(this->name, this_cv_width-3);
}
if (is_enabled(f_cv_output_applied_force)) {
os << " fa_"
<< cvm::wrap_string(this->name, this_cv_width-3);
}
return os;
}
std::ostream & colvar::write_traj(std::ostream &os)
{
os << " ";
if (is_enabled(f_cv_output_value)) {
if (is_enabled(f_cv_extended_Lagrangian)) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< x;
}
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< x_reported;
}
if (is_enabled(f_cv_output_velocity)) {
if (is_enabled(f_cv_extended_Lagrangian)) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< v_fdiff;
}
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< v_reported;
}
if (is_enabled(f_cv_output_energy)) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< potential_energy
<< " "
<< kinetic_energy;
}
if (is_enabled(f_cv_output_total_force)) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< ft_reported;
}
if (is_enabled(f_cv_output_applied_force)) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< applied_force();
}
return os;
}
int colvar::write_output_files()
{
if (cvm::b_analysis) {
if (acf.size()) {
cvm::log("Writing acf to file \""+acf_outfile+"\".\n");
cvm::backup_file(acf_outfile.c_str());
std::ostream *acf_os = cvm::proxy->output_stream(acf_outfile);
if (!acf_os) return cvm::get_error();
write_acf(*acf_os);
cvm::proxy->close_output_stream(acf_outfile);
}
if (runave_os) {
cvm::proxy->close_output_stream(runave_outfile);
runave_os = NULL;
}
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
// ******************** ANALYSIS FUNCTIONS ********************
void colvar::analyze()
{
if (is_enabled(f_cv_runave)) {
calc_runave();
}
if (is_enabled(f_cv_corrfunc)) {
calc_acf();
}
}
inline void history_add_value(size_t const &history_length,
std::list<colvarvalue> &history,
colvarvalue const &new_value)
{
history.push_front(new_value);
if (history.size() > history_length)
history.pop_back();
}
inline void history_incr(std::list< std::list<colvarvalue> > &history,
std::list< std::list<colvarvalue> >::iterator &history_p)
{
if ((++history_p) == history.end())
history_p = history.begin();
}
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
// contain up to acf_length values, which are contiguous in memory
// representation but separated by acf_stride in the time series;
// the pointer to each vector is changed at every step
if (acf_x_history.empty() && acf_v_history.empty()) {
// first-step operations
colvar *cfcv = (acf_colvar_name.size() ?
cvm::colvar_by_name(acf_colvar_name) :
this);
if (colvarvalue::check_types(cfcv->value(), value())) {
cvm::error("Error: correlation function between \""+cfcv->name+
"\" and \""+this->name+"\" cannot be calculated, "
"because their value types are different.\n",
INPUT_ERROR);
}
acf_nframes = 0;
cvm::log("Colvar \""+this->name+"\": initializing ACF calculation.\n");
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 (i = 0; i < acf_stride; i++) {
acf_v_history.push_back(std::list<colvarvalue>());
}
acf_v_history_p = acf_v_history.begin();
break;
case acf_coor:
case acf_p2coor:
// allocate space for the coordinates history
for (i = 0; i < acf_stride; i++) {
acf_x_history.push_back(std::list<colvarvalue>());
}
acf_x_history_p = acf_x_history.begin();
break;
default:
break;
}
} else {
colvar *cfcv = (acf_colvar_name.size() ?
cvm::colvar_by_name(acf_colvar_name) :
this);
switch (acf_type) {
case acf_vel:
if (is_enabled(f_cv_fdiff_velocity)) {
// calc() should do this already, but this only happens in a
// simulation; better do it again in case a trajectory is
// being read
v_reported = v_fdiff = fdiff_velocity(x_old, cfcv->value());
}
calc_vel_acf((*acf_v_history_p), cfcv->velocity());
// store this value in the history
history_add_value(acf_length+acf_offset, *acf_v_history_p, cfcv->velocity());
// if stride is larger than one, cycle among different histories
history_incr(acf_v_history, acf_v_history_p);
break;
case acf_coor:
calc_coor_acf((*acf_x_history_p), cfcv->value());
history_add_value(acf_length+acf_offset, *acf_x_history_p, cfcv->value());
history_incr(acf_x_history, acf_x_history_p);
break;
case acf_p2coor:
calc_p2coor_acf((*acf_x_history_p), cfcv->value());
history_add_value(acf_length+acf_offset, *acf_x_history_p, cfcv->value());
history_incr(acf_x_history, acf_x_history_p);
break;
default:
break;
}
}
if (is_enabled(f_cv_fdiff_velocity)) {
// set it for the next step
x_old = x;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
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
// length is sufficient to hold an entire row of ACF values
if (v_list.size() >= acf_length+acf_offset) {
std::list<colvarvalue>::iterator vs_i = v_list.begin();
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
++vs_i;
// current vel with itself
*(acf_i) += v.norm2();
++acf_i;
// inner products of previous velocities with current (acf_i and
// vs_i are updated)
colvarvalue::inner_opt(v, vs_i, v_list.end(), acf_i);
acf_nframes++;
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
void colvar::calc_coor_acf(std::list<colvarvalue> &x_list,
colvarvalue const &x)
{
// same as above but for coordinates
if (x_list.size() >= acf_length+acf_offset) {
std::list<colvarvalue>::iterator xs_i = x_list.begin();
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
++xs_i;
*(acf_i++) += x.norm2();
colvarvalue::inner_opt(x, xs_i, x_list.end(), acf_i);
acf_nframes++;
}
}
void colvar::calc_p2coor_acf(std::list<colvarvalue> &x_list,
colvarvalue const &x)
{
// same as above but with second order Legendre polynomial instead
// of just the scalar product
if (x_list.size() >= acf_length+acf_offset) {
std::list<colvarvalue>::iterator xs_i = x_list.begin();
std::vector<cvm::real>::iterator acf_i = acf.begin();
for (size_t i = 0; i < acf_offset; i++)
++xs_i;
// value of P2(0) = 1
*(acf_i++) += 1.0;
colvarvalue::p2leg_opt(x, xs_i, x_list.end(), acf_i);
acf_nframes++;
}
}
void colvar::write_acf(std::ostream &os)
{
if (!acf_nframes)
cvm::log("Warning: ACF was not calculated (insufficient frames).\n");
os.setf(std::ios::scientific, std::ios::floatfield);
os << "# Autocorrelation function for collective variable \""
<< this->name << "\"\n";
// one frame is used for normalization, the statistical sample is
// hence decreased
os << "# nframes = " << (acf_normalize ?
acf_nframes - 1 :
acf_nframes) << "\n";
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) {
os << std::setw(cvm::it_width) << acf_stride * (it++) << " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< ( acf_normalize ?
(*acf_i)/(acf_norm * cvm::real(acf_nframes)) :
(*acf_i)/(cvm::real(acf_nframes)) ) << "\n";
}
}
void colvar::calc_runave()
{
if (x_history.empty()) {
runave.type(value().type());
runave.reset();
// first-step operations
if (cvm::debug())
cvm::log("Colvar \""+this->name+
"\": initializing running average calculation.\n");
acf_nframes = 0;
x_history.push_back(std::list<colvarvalue>());
x_history_p = x_history.begin();
} else {
if ( (cvm::step_relative() % runave_stride) == 0) {
if ((*x_history_p).size() >= runave_length-1) {
runave = x;
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);
runave.apply_constraints();
runave_variance = 0.0;
runave_variance += this->dist2(x, runave);
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);
*runave_os << std::setw(cvm::it_width) << cvm::step_relative()
<< " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< runave << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< std::sqrt(runave_variance) << "\n";
}
history_add_value(runave_length, *x_history_p, x);
}
}
}
// Static members
std::vector<colvardeps::feature *> colvar::cv_features;
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