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lammps/lib/colvars/colvar.cpp
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colvar.cpp
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// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
#include "colvarscript.h"
#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(std::string const &conf)
: colvarparse(conf)
{
cvm::log("Initializing a new collective variable.\n");
int error_code = COLVARS_OK;
get_keyval(conf, "name", this->name,
(std::string("colvar")+cvm::to_str(cvm::colvars.size()+1)));
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);
return;
}
// Initialize dependency members
// Could be a function defined in a different source file, for space?
this->description = "colvar " + this->name;
// Initialize static array once and for all
init_cv_requires();
kinetic_energy = 0.0;
potential_energy = 0.0;
cvm::combine_errors(error_code, init_components(conf));
size_t i;
// Setup colvar as scripted function of components
if (get_keyval(conf, "scriptedFunction", scripted_function,
"", colvarparse::parse_silent)) {
// Make feature available only on user request
provide(f_cv_scripted);
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.");
return;
}
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.");
return;
}
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)) {
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);
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");
}
}
}
feature_states[f_cv_linear]->enabled = lin;
}
// Colvar is homogeneous iff:
// - 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;
}
}
feature_states[f_cv_homogeneous]->enabled = homogeneous;
}
// Colvar is deemed periodic iff:
// - it is homogeneous
// - all cvcs are periodic
// - all cvcs have the same period
b_periodic = cvcs[0]->b_periodic && is_enabled(f_cv_homogeneous);
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;
}
}
feature_states[f_cv_periodic]->enabled = b_periodic;
// check that cvcs are compatible
for (i = 0; i < cvcs.size(); i++) {
if ((cvcs[i])->b_periodic && !b_periodic) {
cvm::log("Warning: although this component is periodic, the colvar will "
"not be treated as periodic, either because the exponent is not "
"1, or because multiple components are present. Make sure that "
"you know what you are doing!");
}
// components may have different types only for scripted functions
if (!is_enabled(f_cv_scripted) && (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;
}
}
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());
f_accumulated.type(value());
fb.type(value());
get_keyval(conf, "width", width, 1.0);
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
}
// NOTE: not porting wall stuff to new deps, as this will change to a separate bias
// the grid functions will wait a little as well
lower_boundary.type(value());
lower_wall.type(value());
upper_boundary.type(value());
upper_wall.type(value());
feature_states[f_cv_scalar]->enabled = (value().type() == colvarvalue::type_scalar);
if (is_enabled(f_cv_scalar)) {
if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) {
provide(f_cv_lower_boundary);
enable(f_cv_lower_boundary);
}
get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0);
if (lower_wall_k > 0.0) {
get_keyval(conf, "lowerWall", lower_wall, lower_boundary);
enable(f_cv_lower_wall);
}
if (get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary)) {
provide(f_cv_upper_boundary);
enable(f_cv_upper_boundary);
}
get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0);
if (upper_wall_k > 0.0) {
get_keyval(conf, "upperWall", upper_wall, upper_boundary);
enable(f_cv_upper_wall);
}
}
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);
}
}
if (is_enabled(f_cv_lower_wall) && is_enabled(f_cv_upper_wall)) {
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);
}
}
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);
}
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);
}
get_keyval(conf, "timeStepFactor", time_step_factor, 1);
{
bool b_extended_Lagrangian;
get_keyval(conf, "extendedLagrangian", b_extended_Lagrangian, false);
if (b_extended_Lagrangian) {
cvm::real temp, tolerance, period;
cvm::log("Enabling the extended Lagrangian term for colvar \""+
this->name+"\".\n");
// Make feature available only on user request
provide(f_cv_extended_Lagrangian);
enable(f_cv_extended_Lagrangian);
provide(f_cv_Langevin);
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);
}
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::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)");
{
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);
}
if (ext_gamma != 0.0) {
enable(f_cv_Langevin);
ext_gamma *= 1.0e-3; // convert from ps-1 to fs-1
ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / cvm::dt());
}
}
}
{
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 b_output_system_force;
get_keyval(conf, "outputSystemForce", b_output_system_force, false);
if (b_output_system_force) {
enable(f_cv_output_system_force);
}
}
{
bool b_output_applied_force;
get_keyval(conf, "outputAppliedForce", b_output_applied_force, false);
if (b_output_applied_force) {
enable(f_cv_output_applied_force);
}
}
// Start in active state by default
enable(f_cv_active);
// Make sure dependency side-effects are correct
refresh_deps();
x_old.type(value());
v_fdiff.type(value());
v_reported.type(value());
fj.type(value());
ft.type(value());
ft_reported.type(value());
if (cvm::b_analysis)
parse_analysis(conf);
if (cvm::debug())
cvm::log("Done initializing collective variable \""+this->name+"\".\n");
}
// 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("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;
cvm::combine_errors(error_code,
init_components_type<distance>(conf,
"distance", "distance"));
cvm::combine_errors(error_code,
init_components_type<distance_vec>(conf,
"distance vector", "distanceVec"));
cvm::combine_errors(error_code,
init_components_type<cartesian>(conf,
"Cartesian coordinates", "cartesian"));
cvm::combine_errors(error_code,
init_components_type<distance_dir>(conf,
"distance vector "
"direction", "distanceDir"));
cvm::combine_errors(error_code,
init_components_type<distance_z>(conf,
"distance projection "
"on an axis", "distanceZ"));
cvm::combine_errors(error_code,
init_components_type<distance_xy>(conf,
"distance projection "
"on a plane", "distanceXY"));
cvm::combine_errors(error_code,
init_components_type<distance_inv>(conf,
"average distance "
"weighted by inverse power",
"distanceInv"));
cvm::combine_errors(error_code,
init_components_type<distance_pairs>(conf,
"N1xN2-long vector "
"of pairwise distances",
"distancePairs"));
cvm::combine_errors(error_code,
init_components_type<coordnum>(conf,
"coordination "
"number", "coordNum"));
cvm::combine_errors(error_code,
init_components_type<selfcoordnum>(conf,
"self-coordination "
"number", "selfCoordNum"));
cvm::combine_errors(error_code,
init_components_type<angle>(conf,
"angle", "angle"));
cvm::combine_errors(error_code,
init_components_type<dipole_angle>(conf,
"dipole angle", "dipoleAngle"));
cvm::combine_errors(error_code,
init_components_type<dihedral>(conf,
"dihedral", "dihedral"));
cvm::combine_errors(error_code,
init_components_type<h_bond>(conf,
"hydrogen bond", "hBond"));
// cvm::combine_errors(error_code, init_components_type<alpha_dihedrals>(conf, "alpha helix", "alphaDihedrals"));
cvm::combine_errors(error_code,
init_components_type<alpha_angles>(conf,
"alpha helix", "alpha"));
cvm::combine_errors(error_code,
init_components_type<dihedPC>(conf,
"dihedral "
"principal component", "dihedralPC"));
cvm::combine_errors(error_code,
init_components_type<orientation>(conf,
"orientation", "orientation"));
cvm::combine_errors(error_code,
init_components_type<orientation_angle>(conf,
"orientation "
"angle", "orientationAngle"));
cvm::combine_errors(error_code,
init_components_type<orientation_proj>(conf,
"orientation "
"projection", "orientationProj"));
cvm::combine_errors(error_code,
init_components_type<tilt>(conf,
"tilt", "tilt"));
cvm::combine_errors(error_code,
init_components_type<spin_angle>(conf,
"spin angle", "spinAngle"));
cvm::combine_errors(error_code,
init_components_type<rmsd>(conf,
"RMSD", "rmsd"));
// cvm::combine_errors(error_code, init_components_type <logmsd>(conf,"logarithm of MSD", "logmsd"));
cvm::combine_errors(error_code,
init_components_type<gyration>(conf,
"radius of "
"gyration", "gyration"));
cvm::combine_errors(error_code,
init_components_type<inertia>(conf,
"moment of "
"inertia", "inertia"));
cvm::combine_errors(error_code,
init_components_type<inertia_z>(conf,
"moment of inertia around an axis",
"inertiaZ"));
cvm::combine_errors(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;
}
int colvar::refresh_deps()
{
// If enabled features are changed upstream, the features below should be refreshed
if (is_enabled(f_cv_system_force_calc)) {
cvm::request_system_force();
}
if (is_enabled(f_cv_collect_gradient) && atom_ids.size() == 0) {
build_atom_list();
}
return COLVARS_OK;
}
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);
}
std::string runave_outfile;
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::backup_file(runave_outfile.c_str());
runave_os.open(runave_outfile.c_str());
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_bit(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()
{
// 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
for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin();
cvi != cvm::colvars.end();
++cvi) {
if ( *cvi == this) {
cvm::colvars.erase(cvi);
break;
}
}
}
// ******************** 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)) {
cvm::combine_errors(error_code, update_cvc_flags());
cvm::combine_errors(error_code, calc_cvcs());
cvm::combine_errors(error_code, collect_cvc_data());
}
return error_code;
}
int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
{
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");
cvm::combine_errors(error_code, check_cvc_range(first_cvc, num_cvcs));
if (error_code != COLVARS_OK) {
return error_code;
}
cvm::combine_errors(error_code, calc_cvc_values(first_cvc, num_cvcs));
cvm::combine_errors(error_code, calc_cvc_gradients(first_cvc, num_cvcs));
cvm::combine_errors(error_code, calc_cvc_sys_forces(first_cvc, num_cvcs));
cvm::combine_errors(error_code, calc_cvc_Jacobians(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;
cvm::combine_errors(error_code, collect_cvc_values());
cvm::combine_errors(error_code, collect_cvc_gradients());
cvm::combine_errors(error_code, collect_cvc_sys_forces());
cvm::combine_errors(error_code, collect_cvc_Jacobians());
cvm::combine_errors(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();
size_t i;
// 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;
}
} else if (x.type() == colvarvalue::type_scalar) {
// polynomial combination allowed
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->is_enabled()) continue;
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 );
}
} else {
for (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");
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 (is_enabled(f_cv_gradient)) {
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++;
(cvcs[i])->calc_gradients();
// 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++) {
if (cvcs[i]->atom_groups[ig]->b_fit_gradients)
cvcs[i]->atom_groups[ig]->calc_fit_gradients();
if (cvcs[i]->is_enabled(f_cvc_debug_gradient)) {
cvm::log("Debugging gradients for " + cvcs[i]->description);
cvcs[i]->debug_gradients(cvcs[i]->atom_groups[ig]);
}
}
}
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)) {
if (is_enabled(f_cv_scripted)) {
cvm::error("Collecting atomic gradients is not implemented for "
"scripted colvars.", COLVARS_NOT_IMPLEMENTED);
return COLVARS_NOT_IMPLEMENTED;
}
// 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) *
std::pow((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_sys_forces(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_system_force_calc)) {
if (cvm::debug())
cvm::log("Calculating system force of colvar \""+this->name+"\".\n");
// 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) {
cvm::increase_depth();
// get from the cvcs the system forces from the PREVIOUS step
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 system force of colvar \""+this->name+"\".\n");
}
return COLVARS_OK;
}
int colvar::collect_cvc_sys_forces()
{
if (is_enabled(f_cv_system_force_calc)) {
ft.reset();
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++) {
if (!cvcs[i]->is_enabled()) continue;
// linear combination is assumed
ft += (cvcs[i])->system_force() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
}
}
if (!is_enabled(f_cv_hide_Jacobian)) {
// add the Jacobian force to the system 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;
// 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
// TODO: put it in the restart information
if (cvm::step_relative() == 0) {
xr = x;
vr = 0.0; // (already 0; added for clarity)
}
// report the restraint center as "value"
x_reported = xr;
v_reported = vr;
// the "system force" with the extended Lagrangian is just the
// harmonic term acting on the extended coordinate
// Note: this is the force for current timestep
ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
} else {
x_reported = x;
ft_reported = ft;
}
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();
// 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 system force;
// instead, it is subtracted from the applied force (silent Jacobian correction)
if (is_enabled(f_cv_hide_Jacobian))
f -= fj;
}
if (is_enabled(f_cv_extended_Lagrangian)) {
cvm::real dt = cvm::dt();
cvm::real f_ext;
// the total force is applied to the fictitious mass, while the
// atoms only feel the harmonic force
// fr: bias force on extended coordinate (without harmonic spring), for output in trajectory
// f_ext: total force on extended coordinate (including harmonic spring)
// f: - initially, external biasing force
// - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
// (note: wall potential is added to f after this block)
fr = f;
f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
// 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.real_value;
vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
}
vr += (0.5 * dt) * f_ext / ext_mass;
xr += dt * vr;
xr.apply_constraints();
if (this->b_periodic) this->wrap(xr);
}
// Adding wall potential to "true" colvar force, whether or not an extended coordinate is in use
if (is_enabled(f_cv_lower_wall) || is_enabled(f_cv_upper_wall)) {
// Wall force
colvarvalue fw(x);
fw.reset();
if (cvm::debug())
cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n");
// For a periodic colvar, both walls may be applicable at the same time
// in which case we pick the closer one
if ( (!is_enabled(f_cv_upper_wall)) ||
(this->dist2(x, lower_wall) < this->dist2(x, upper_wall)) ) {
cvm::real const grad = this->dist2_lgrad(x, lower_wall);
if (grad < 0.0) {
fw = -0.5 * lower_wall_k * grad;
f += fw;
if (cvm::debug())
cvm::log("Applying a lower wall force("+
cvm::to_str(fw)+") to \""+this->name+"\".\n");
}
} else {
cvm::real const grad = this->dist2_lgrad(x, upper_wall);
if (grad > 0.0) {
fw = -0.5 * upper_wall_k * grad;
f += fw;
if (cvm::debug())
cvm::log("Applying an upper wall force("+
cvm::to_str(fw)+") to \""+this->name+"\".\n");
}
}
}
f_accumulated += f;
if (is_enabled(f_cv_fdiff_velocity)) {
// set it for the next step
x_old = x;
}
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");
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_accumulated.as_vector() * func_grads[grad_index++],
cvcs[i]->value().type()));
}
} 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_accumulated * (cvcs[i])->sup_coeff *
cvm::real((cvcs[i])->sup_np) *
(std::pow((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_accumulated * (cvcs[i])->sup_coeff);
}
}
// Accumulated forces have been applied, impulse-style
// Reset to start accumulating again
f_accumulated.reset();
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]->feature_states[f_cvc_active]->enabled = 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.resize(0);
}
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_bit(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,
colvarvalue(x.type()), 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");
}
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_system_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_system_force)) {
os << " fs_"
<< 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_system_force)) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< ft_reported;
}
if (is_enabled(f_cv_output_applied_force)) {
if (is_enabled(f_cv_extended_Lagrangian)) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< fr;
} else {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< f;
}
}
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());
cvm::ofstream acf_os(acf_outfile.c_str());
if (! acf_os.is_open()) {
cvm::error("Cannot open file \""+acf_outfile+"\".\n", FILE_ERROR);
}
write_acf(acf_os);
acf_os.close();
}
if (runave_os.is_open()) {
runave_os.close();
}
}
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<cvm::deps::feature *> colvar::cv_features;
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