forked from lijiext/lammps
1673 lines
51 KiB
C++
1673 lines
51 KiB
C++
// -*- c++ -*-
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#include "colvarmodule.h"
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#include "colvarvalue.h"
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#include "colvarparse.h"
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#include "colvar.h"
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#include "colvarcomp.h"
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#include <algorithm>
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// XX TODO make the acf code handle forces as well as values and velocities
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colvar::colvar (std::string const &conf)
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{
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cvm::log ("Initializing a new collective variable.\n");
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get_keyval (conf, "name", this->name,
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(std::string ("colvar")+cvm::to_str (cvm::colvars.size()+1)));
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for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin();
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cvi < cvm::colvars.end();
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cvi++) {
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if ((*cvi)->name == this->name)
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cvm::fatal_error ("Error: this colvar cannot have the same name, \""+this->name+
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"\", as another colvar.\n");
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}
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// all tasks disabled by default
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for (size_t i = 0; i < task_ntot; i++) {
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tasks[i] = false;
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}
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kinetic_energy = 0.0;
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potential_energy = 0.0;
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// read the configuration and set up corresponding instances, for
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// each type of component implemented
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#define initialize_components(def_desc,def_config_key,def_class_name) \
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{ \
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size_t def_count = 0; \
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std::string def_conf = ""; \
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size_t pos = 0; \
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while ( this->key_lookup (conf, \
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def_config_key, \
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def_conf, \
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pos) ) { \
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if (!def_conf.size()) continue; \
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cvm::log ("Initializing " \
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"a new \""+std::string (def_config_key)+"\" component"+ \
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(cvm::debug() ? ", with configuration:\n"+def_conf \
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: ".\n")); \
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cvm::increase_depth(); \
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cvc *cvcp = new colvar::def_class_name (def_conf); \
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if (cvcp != NULL) { \
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cvcs.push_back (cvcp); \
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cvcp->check_keywords (def_conf, def_config_key); \
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cvm::decrease_depth(); \
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} else { \
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cvm::fatal_error ("Error: in allocating component \"" \
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def_config_key"\".\n"); \
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} \
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if ( (cvcp->period != 0.0) || (cvcp->wrap_center != 0.0) ) { \
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if ( (cvcp->function_type != std::string ("distance_z")) && \
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(cvcp->function_type != std::string ("dihedral")) && \
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(cvcp->function_type != std::string ("spin_angle")) ) { \
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cvm::fatal_error ("Error: invalid use of period and/or " \
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"wrapAround in a \""+ \
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std::string (def_config_key)+ \
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"\" component.\n"+ \
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"Period: "+cvm::to_str(cvcp->period) + \
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" wrapAround: "+cvm::to_str(cvcp->wrap_center));\
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} \
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} \
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if ( ! cvcs.back()->name.size()) \
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cvcs.back()->name = std::string (def_config_key)+ \
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(cvm::to_str (++def_count)); \
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if (cvm::debug()) \
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cvm::log ("Done initializing a \""+ \
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std::string (def_config_key)+ \
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"\" component"+ \
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(cvm::debug() ? \
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", named \""+cvcs.back()->name+"\"" \
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: "")+".\n"); \
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def_conf = ""; \
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if (cvm::debug()) \
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cvm::log ("Parsed "+cvm::to_str (cvcs.size())+ \
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" components at this time.\n"); \
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} \
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}
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initialize_components ("distance", "distance", distance);
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initialize_components ("distance vector", "distanceVec", distance_vec);
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initialize_components ("distance vector "
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"direction", "distanceDir", distance_dir);
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initialize_components ("distance projection "
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"on an axis", "distanceZ", distance_z);
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initialize_components ("distance projection "
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"on a plane", "distanceXY", distance_xy);
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initialize_components ("average distance weighted by inverse power",
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"distanceInv", distance_inv);
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initialize_components ("coordination "
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"number", "coordNum", coordnum);
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initialize_components ("self-coordination "
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"number", "selfCoordNum", selfcoordnum);
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initialize_components ("angle", "angle", angle);
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initialize_components ("dihedral", "dihedral", dihedral);
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initialize_components ("hydrogen bond", "hBond", h_bond);
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// initialize_components ("alpha helix", "alphaDihedrals", alpha_dihedrals);
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initialize_components ("alpha helix", "alpha", alpha_angles);
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initialize_components ("dihedral principal "
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"component", "dihedralPC", dihedPC);
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initialize_components ("orientation", "orientation", orientation);
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initialize_components ("orientation "
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"angle", "orientationAngle",orientation_angle);
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initialize_components ("tilt", "tilt", tilt);
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initialize_components ("spin angle", "spinAngle", spin_angle);
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initialize_components ("RMSD", "rmsd", rmsd);
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// initialize_components ("logarithm of MSD", "logmsd", logmsd);
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initialize_components ("radius of "
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"gyration", "gyration", gyration);
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initialize_components ("moment of "
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"inertia", "inertia", inertia);
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initialize_components ("moment of inertia around an axis",
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"inertiaZ", inertia_z);
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initialize_components ("eigenvector", "eigenvector", eigenvector);
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if (!cvcs.size())
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cvm::fatal_error ("Error: no valid components were provided "
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"for this collective variable.\n");
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cvm::log ("All components initialized.\n");
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// this is set false if any of the components has an exponent
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// different from 1 in the polynomial
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b_linear = true;
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// these will be set to false if any of the cvcs has them false
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b_inverse_gradients = true;
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b_Jacobian_force = true;
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// Decide whether the colvar is periodic
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// Used to wrap extended DOF if extendedLagrangian is on
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if (cvcs.size() == 1 && (cvcs[0])->b_periodic && (cvcs[0])->sup_np == 1
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&& (cvcs[0])->sup_coeff == 1.0 ) {
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this->b_periodic = true;
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this->period = (cvcs[0])->period;
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// TODO write explicit wrap() function for colvars to allow for
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// sup_coeff different from 1
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// this->period = (cvcs[0])->period * (cvcs[0])->sup_coeff;
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} else {
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this->b_periodic = false;
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this->period = 0.0;
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}
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// check the available features of each cvc
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for (size_t i = 0; i < cvcs.size(); i++) {
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if ((cvcs[i])->sup_np != 1) {
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if (cvm::debug() && b_linear)
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cvm::log ("Warning: You are using a non-linear polynomial "
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"combination to define this collective variable, "
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"some biasing methods may be unavailable.\n");
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b_linear = false;
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if ((cvcs[i])->sup_np < 0) {
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cvm::log ("Warning: you chose a negative exponent in the combination; "
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"if you apply forces, the simulation may become unstable "
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"when the component \""+
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(cvcs[i])->function_type+"\" approaches zero.\n");
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}
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}
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if ((cvcs[i])->b_periodic && !b_periodic) {
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cvm::log ("Warning: although this component is periodic, the colvar will "
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"not be treated as periodic, either because the exponent is not "
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"1, or because multiple components are present. Make sure that "
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"you know what you are doing!");
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}
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if (! (cvcs[i])->b_inverse_gradients)
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b_inverse_gradients = false;
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if (! (cvcs[i])->b_Jacobian_derivative)
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b_Jacobian_force = false;
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for (size_t j = i; j < cvcs.size(); j++) {
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if ( (cvcs[i])->type() != (cvcs[j])->type() ) {
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cvm::fatal_error ("ERROR: you are definining this collective variable "
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"by using components of different types, \""+
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colvarvalue::type_desc[(cvcs[i])->type()]+
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"\" and \""+
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colvarvalue::type_desc[(cvcs[j])->type()]+
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"\". "
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"You must use the same type in order to "
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" sum them together.\n");
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}
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}
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}
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{
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colvarvalue::Type const value_type = (cvcs[0])->type();
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if (cvm::debug())
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cvm::log ("This collective variable is a "+
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colvarvalue::type_desc[value_type]+", corresponding to "+
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cvm::to_str (colvarvalue::dof_num[value_type])+
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" internal degrees of freedom.\n");
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x.type (value_type);
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x_reported.type (value_type);
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}
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get_keyval (conf, "width", width, 1.0);
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if (width <= 0.0)
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cvm::fatal_error ("Error: \"width\" must be positive.\n");
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lower_boundary.type (this->type());
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lower_wall.type (this->type());
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upper_boundary.type (this->type());
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upper_wall.type (this->type());
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if (this->type() == colvarvalue::type_scalar) {
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if (get_keyval (conf, "lowerBoundary", lower_boundary, lower_boundary)) {
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enable (task_lower_boundary);
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}
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get_keyval (conf, "lowerWallConstant", lower_wall_k, 0.0);
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if (lower_wall_k > 0.0) {
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get_keyval (conf, "lowerWall", lower_wall, lower_boundary);
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enable (task_lower_wall);
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}
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if (get_keyval (conf, "upperBoundary", upper_boundary, upper_boundary)) {
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enable (task_upper_boundary);
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}
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get_keyval (conf, "upperWallConstant", upper_wall_k, 0.0);
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if (upper_wall_k > 0.0) {
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get_keyval (conf, "upperWall", upper_wall, upper_boundary);
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enable (task_upper_wall);
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}
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}
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if (tasks[task_lower_boundary]) {
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get_keyval (conf, "hardLowerBoundary", hard_lower_boundary, false);
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}
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if (tasks[task_upper_boundary]) {
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get_keyval (conf, "hardUpperBoundary", hard_upper_boundary, false);
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}
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// consistency checks for boundaries and walls
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if (tasks[task_lower_boundary] && tasks[task_upper_boundary]) {
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if (lower_boundary >= upper_boundary) {
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cvm::fatal_error ("Error: the upper boundary, "+
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cvm::to_str (upper_boundary)+
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", is not higher than the lower boundary, "+
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cvm::to_str (lower_boundary)+".\n");
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}
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}
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if (tasks[task_lower_wall] && tasks[task_upper_wall]) {
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if (lower_wall >= upper_wall) {
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cvm::fatal_error ("Error: the upper wall, "+
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cvm::to_str (upper_wall)+
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", is not higher than the lower wall, "+
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cvm::to_str (lower_wall)+".\n");
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}
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if (dist2 (lower_wall, upper_wall) < 1.0E-12) {
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cvm::log ("Lower wall and upper wall are equal "
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"in the periodic domain of the colvar: disabling walls.\n");
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disable (task_lower_wall);
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disable (task_upper_wall);
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}
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}
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get_keyval (conf, "expandBoundaries", expand_boundaries, false);
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if (expand_boundaries && periodic_boundaries()) {
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cvm::fatal_error ("Error: trying to expand boundaries that already "
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"cover a whole period of a periodic colvar.\n");
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}
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if (expand_boundaries && hard_lower_boundary && hard_upper_boundary) {
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cvm::fatal_error ("Error: inconsistent configuration "
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"(trying to expand boundaries with both "
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"hardLowerBoundary and hardUpperBoundary enabled).\n");
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}
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{
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bool b_extended_lagrangian;
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get_keyval (conf, "extendedLagrangian", b_extended_lagrangian, false);
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if (b_extended_lagrangian) {
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cvm::real temp, tolerance, period;
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cvm::log ("Enabling the extended Lagrangian term for colvar \""+
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this->name+"\".\n");
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enable (task_extended_lagrangian);
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xr.type (this->type());
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vr.type (this->type());
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fr.type (this->type());
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const bool found = get_keyval (conf, "extendedTemp", temp, cvm::temperature());
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if (temp <= 0.0) {
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if (found)
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cvm::fatal_error ("Error: \"extendedTemp\" must be positive.\n");
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else
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cvm::fatal_error ("Error: a positive temperature must be provided, either "
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"by enabling a thermostat, or through \"extendedTemp\".\n");
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}
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get_keyval (conf, "extendedFluctuation", tolerance, width);
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if (tolerance <= 0.0)
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cvm::fatal_error ("Error: \"extendedFluctuation\" must be positive.\n");
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ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
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cvm::log ("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " kcal/mol/U^2");
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get_keyval (conf, "extendedTimeConstant", period, 200.0);
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if (period <= 0.0)
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cvm::fatal_error ("Error: \"extendedTimeConstant\" must be positive.\n");
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ext_mass = (cvm::boltzmann() * temp * period * period)
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/ (4.0 * PI * PI * tolerance * tolerance);
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cvm::log ("Computed fictitious mass: " + cvm::to_str(ext_mass) + " kcal/mol/(U/fs)^2 (U: colvar unit)");
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{
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bool b_output_energy;
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get_keyval (conf, "outputEnergy", b_output_energy, false);
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if (b_output_energy) {
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enable (task_output_energy);
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}
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}
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get_keyval (conf, "extendedLangevinDamping", ext_gamma, 1.0);
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if (ext_gamma < 0.0)
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cvm::fatal_error ("Error: \"extendedLangevinDamping\" may not be negative.\n");
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if (ext_gamma != 0.0) {
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enable (task_langevin);
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ext_gamma *= 1.0e-3; // convert from ps-1 to fs-1
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ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / cvm::dt());
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}
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}
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}
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{
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bool b_output_value;
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get_keyval (conf, "outputValue", b_output_value, true);
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if (b_output_value) {
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enable (task_output_value);
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}
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}
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{
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bool b_output_velocity;
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get_keyval (conf, "outputVelocity", b_output_velocity, false);
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if (b_output_velocity) {
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enable (task_output_velocity);
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}
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}
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{
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bool b_output_system_force;
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get_keyval (conf, "outputSystemForce", b_output_system_force, false);
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if (b_output_system_force) {
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enable (task_output_system_force);
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}
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}
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{
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bool b_output_applied_force;
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get_keyval (conf, "outputAppliedForce", b_output_applied_force, false);
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if (b_output_applied_force) {
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enable (task_output_applied_force);
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}
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}
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if (cvm::b_analysis)
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parse_analysis (conf);
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if (cvm::debug())
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cvm::log ("Done initializing collective variable \""+this->name+"\".\n");
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}
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void colvar::build_atom_list (void)
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{
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// If atomic gradients are requested, build full list of atom ids from all cvcs
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std::list<int> temp_id_list;
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for (size_t i = 0; i < cvcs.size(); i++) {
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for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) {
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for (size_t k = 0; k < cvcs[i]->atom_groups[j]->size(); k++) {
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temp_id_list.push_back (cvcs[i]->atom_groups[j]->at(k).id);
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}
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}
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}
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temp_id_list.sort();
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temp_id_list.unique();
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atom_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
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temp_id_list.clear();
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atomic_gradients.resize (atom_ids.size());
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if (atom_ids.size()) {
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if (cvm::debug())
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cvm::log ("Colvar: created atom list with " + cvm::to_str(atom_ids.size()) + " atoms.\n");
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} else {
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cvm::log ("Warning: colvar components communicated no atom IDs.\n");
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}
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}
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void colvar::parse_analysis (std::string const &conf)
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{
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// if (cvm::debug())
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// cvm::log ("Parsing analysis flags for collective variable \""+
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// this->name+"\".\n");
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runave_length = 0;
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bool b_runave = false;
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if (get_keyval (conf, "runAve", b_runave) && b_runave) {
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enable (task_runave);
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get_keyval (conf, "runAveLength", runave_length, 1000);
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get_keyval (conf, "runAveStride", runave_stride, 1);
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if ((cvm::restart_out_freq % runave_stride) != 0)
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cvm::fatal_error ("Error: runAveStride must be commensurate with the restart frequency.\n");
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std::string runave_outfile;
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get_keyval (conf, "runAveOutputFile", runave_outfile,
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std::string (cvm::output_prefix+"."+
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this->name+".runave.traj"));
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size_t const this_cv_width = x.output_width (cvm::cv_width);
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runave_os.open (runave_outfile.c_str());
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runave_os << "# " << cvm::wrap_string ("step", cvm::it_width-2)
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<< " "
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<< cvm::wrap_string ("running average", this_cv_width)
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<< " "
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<< cvm::wrap_string ("running stddev", this_cv_width)
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<< "\n";
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}
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acf_length = 0;
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bool b_acf = false;
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if (get_keyval (conf, "corrFunc", b_acf) && b_acf) {
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enable (task_corrfunc);
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std::string acf_colvar_name;
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get_keyval (conf, "corrFuncWithColvar", acf_colvar_name, this->name);
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if (acf_colvar_name == this->name) {
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cvm::log ("Calculating auto-correlation function.\n");
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} else {
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cvm::log ("Calculating correlation function with \""+
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this->name+"\".\n");
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}
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std::string acf_type_str;
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get_keyval (conf, "corrFuncType", acf_type_str, to_lower_cppstr (std::string ("velocity")));
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if (acf_type_str == to_lower_cppstr (std::string ("coordinate"))) {
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|
acf_type = acf_coor;
|
|
} else if (acf_type_str == to_lower_cppstr (std::string ("velocity"))) {
|
|
acf_type = acf_vel;
|
|
enable (task_fdiff_velocity);
|
|
if (acf_colvar_name.size())
|
|
(cvm::colvar_p (acf_colvar_name))->enable (task_fdiff_velocity);
|
|
} else if (acf_type_str == to_lower_cppstr (std::string ("coordinate_p2"))) {
|
|
acf_type = acf_p2coor;
|
|
} else {
|
|
cvm::fatal_error ("Unknown type of correlation function, \""+
|
|
acf_type_str+"\".\n");
|
|
}
|
|
|
|
get_keyval (conf, "corrFuncOffset", acf_offset, 0);
|
|
get_keyval (conf, "corrFuncLength", acf_length, 1000);
|
|
get_keyval (conf, "corrFuncStride", acf_stride, 1);
|
|
|
|
if ((cvm::restart_out_freq % acf_stride) != 0)
|
|
cvm::fatal_error ("Error: corrFuncStride must be commensurate with the restart frequency.\n");
|
|
|
|
get_keyval (conf, "corrFuncNormalize", acf_normalize, true);
|
|
get_keyval (conf, "corrFuncOutputFile", acf_outfile,
|
|
std::string (cvm::output_prefix+"."+this->name+
|
|
".corrfunc.dat"));
|
|
}
|
|
}
|
|
|
|
|
|
void colvar::enable (colvar::task const &t)
|
|
{
|
|
switch (t) {
|
|
|
|
case task_output_system_force:
|
|
enable (task_system_force);
|
|
break;
|
|
|
|
case task_report_Jacobian_force:
|
|
enable (task_Jacobian_force);
|
|
enable (task_system_force);
|
|
if (cvm::debug())
|
|
cvm::log ("Adding the Jacobian force to the system force, "
|
|
"rather than applying its opposite silently.\n");
|
|
break;
|
|
|
|
case task_Jacobian_force:
|
|
// checks below do not apply to extended-system colvars
|
|
if ( !tasks[task_extended_lagrangian] ) {
|
|
enable (task_gradients);
|
|
|
|
if (!b_Jacobian_force)
|
|
cvm::fatal_error ("Error: colvar \""+this->name+
|
|
"\" does not have Jacobian forces implemented.\n");
|
|
if (!b_linear)
|
|
cvm::fatal_error ("Error: colvar \""+this->name+
|
|
"\" must be defined as a linear combination "
|
|
"to calculate the Jacobian force.\n");
|
|
if (cvm::debug())
|
|
cvm::log ("Enabling calculation of the Jacobian force "
|
|
"on this colvar.\n");
|
|
}
|
|
fj.type (this->type());
|
|
break;
|
|
|
|
case task_system_force:
|
|
if (!tasks[task_extended_lagrangian]) {
|
|
if (!b_inverse_gradients) {
|
|
cvm::fatal_error ("Error: one or more of the components of "
|
|
"colvar \""+this->name+
|
|
"\" does not support system force calculation.\n");
|
|
}
|
|
cvm::request_system_force();
|
|
}
|
|
ft.type (this->type());
|
|
ft_reported.type (this->type());
|
|
break;
|
|
|
|
case task_output_applied_force:
|
|
case task_lower_wall:
|
|
case task_upper_wall:
|
|
// all of the above require gradients
|
|
enable (task_gradients);
|
|
break;
|
|
|
|
case task_fdiff_velocity:
|
|
x_old.type (this->type());
|
|
v_fdiff.type (this->type());
|
|
v_reported.type (this->type());
|
|
break;
|
|
|
|
case task_output_velocity:
|
|
enable (task_fdiff_velocity);
|
|
break;
|
|
|
|
case task_grid:
|
|
if (this->type() != colvarvalue::type_scalar)
|
|
cvm::fatal_error ("Cannot calculate a grid for collective variable, \""+
|
|
this->name+"\", because its value is not a scalar number.\n");
|
|
break;
|
|
|
|
case task_extended_lagrangian:
|
|
enable (task_gradients);
|
|
v_reported.type (this->type());
|
|
break;
|
|
|
|
case task_lower_boundary:
|
|
case task_upper_boundary:
|
|
if (this->type() != colvarvalue::type_scalar) {
|
|
cvm::fatal_error ("Error: this colvar is not a scalar value "
|
|
"and cannot produce a grid.\n");
|
|
}
|
|
break;
|
|
|
|
|
|
case task_output_value:
|
|
case task_runave:
|
|
case task_corrfunc:
|
|
case task_ntot:
|
|
break;
|
|
|
|
case task_gradients:
|
|
f.type (this->type());
|
|
fb.type (this->type());
|
|
break;
|
|
|
|
case task_collect_gradients:
|
|
if (this->type() != colvarvalue::type_scalar)
|
|
cvm::fatal_error ("Collecting atomic gradients for non-scalar collective variable \""+
|
|
this->name+"\" is not yet implemented.\n");
|
|
enable (task_gradients);
|
|
if (atom_ids.size() == 0) {
|
|
build_atom_list();
|
|
}
|
|
break;
|
|
}
|
|
|
|
|
|
tasks[t] = true;
|
|
}
|
|
|
|
|
|
void colvar::disable (colvar::task const &t)
|
|
{
|
|
// check dependencies
|
|
switch (t) {
|
|
case task_gradients:
|
|
disable (task_upper_wall);
|
|
disable (task_lower_wall);
|
|
disable (task_output_applied_force);
|
|
disable (task_system_force);
|
|
disable (task_Jacobian_force);
|
|
break;
|
|
|
|
case task_system_force:
|
|
disable (task_output_system_force);
|
|
break;
|
|
|
|
case task_Jacobian_force:
|
|
disable (task_report_Jacobian_force);
|
|
break;
|
|
|
|
case task_fdiff_velocity:
|
|
disable (task_output_velocity);
|
|
break;
|
|
|
|
case task_lower_boundary:
|
|
case task_upper_boundary:
|
|
disable (task_grid);
|
|
break;
|
|
|
|
case task_extended_lagrangian:
|
|
case task_report_Jacobian_force:
|
|
case task_output_value:
|
|
case task_output_velocity:
|
|
case task_output_applied_force:
|
|
case task_output_system_force:
|
|
case task_runave:
|
|
case task_corrfunc:
|
|
case task_grid:
|
|
case task_lower_wall:
|
|
case task_upper_wall:
|
|
case task_ntot:
|
|
break;
|
|
}
|
|
|
|
tasks[t] = false;
|
|
}
|
|
|
|
|
|
colvar::~colvar()
|
|
{
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
delete cvcs[i];
|
|
}
|
|
}
|
|
|
|
|
|
|
|
// ******************** CALC FUNCTIONS ********************
|
|
|
|
|
|
void colvar::calc()
|
|
{
|
|
if (cvm::debug())
|
|
cvm::log ("Calculating colvar \""+this->name+"\".\n");
|
|
|
|
// prepare atom groups for calculation
|
|
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.reset_atoms_data();
|
|
atoms.read_positions();
|
|
if (atoms.b_center || atoms.b_rotate) {
|
|
atoms.calc_apply_roto_translation();
|
|
}
|
|
// each atom group will take care of its own ref_pos_group, if defined
|
|
}
|
|
}
|
|
if (tasks[task_output_velocity]) {
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
|
|
cvcs[i]->atom_groups[ig]->read_velocities();
|
|
}
|
|
}
|
|
}
|
|
if (tasks[task_system_force]) {
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
|
|
cvcs[i]->atom_groups[ig]->read_system_forces();
|
|
}
|
|
}
|
|
}
|
|
|
|
// calculate the value of the colvar
|
|
|
|
x.reset();
|
|
if (x.type() == colvarvalue::type_scalar) {
|
|
// polynomial combination allowed
|
|
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
cvm::increase_depth();
|
|
(cvcs[i])->calc_value();
|
|
cvm::decrease_depth();
|
|
if (cvm::debug())
|
|
cvm::log ("Colvar component no. "+cvm::to_str (i+1)+
|
|
" within colvar \""+this->name+"\" has value "+
|
|
cvm::to_str ((cvcs[i])->value(),
|
|
cvm::cv_width, cvm::cv_prec)+".\n");
|
|
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 {
|
|
// only linear combination allowed
|
|
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
cvm::increase_depth();
|
|
(cvcs[i])->calc_value();
|
|
cvm::decrease_depth();
|
|
if (cvm::debug())
|
|
cvm::log ("Colvar component no. "+cvm::to_str (i+1)+
|
|
" within colvar \""+this->name+"\" has value "+
|
|
cvm::to_str ((cvcs[i])->value(),
|
|
cvm::cv_width, cvm::cv_prec)+".\n");
|
|
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 (tasks[task_gradients]) {
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Calculating gradients of colvar \""+this->name+"\".\n");
|
|
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
// calculate the gradients of each component
|
|
cvm::increase_depth();
|
|
|
|
(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();
|
|
}
|
|
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Done calculating gradients of colvar \""+this->name+"\".\n");
|
|
|
|
if (tasks[task_collect_gradients]) {
|
|
// Collect the atomic gradients inside colvar object
|
|
for (int a = 0; a < atomic_gradients.size(); a++) {
|
|
atomic_gradients[a].reset();
|
|
}
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
// Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
|
|
cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real ((cvcs[i])->sup_np) *
|
|
std::pow ((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);
|
|
|
|
for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) {
|
|
|
|
// If necessary, apply inverse rotation to get atomic
|
|
// gradient in the laboratory frame
|
|
if (cvcs[i]->atom_groups[j]->b_rotate) {
|
|
cvm::rotation const rot_inv = cvcs[i]->atom_groups[j]->rot.inverse();
|
|
|
|
for (size_t k = 0; k < cvcs[i]->atom_groups[j]->size(); k++) {
|
|
int a = std::lower_bound (atom_ids.begin(), atom_ids.end(),
|
|
cvcs[i]->atom_groups[j]->at(k).id) - atom_ids.begin();
|
|
atomic_gradients[a] += coeff *
|
|
rot_inv.rotate (cvcs[i]->atom_groups[j]->at(k).grad);
|
|
}
|
|
|
|
} else {
|
|
|
|
for (size_t k = 0; k < cvcs[i]->atom_groups[j]->size(); k++) {
|
|
int a = std::lower_bound (atom_ids.begin(), atom_ids.end(),
|
|
cvcs[i]->atom_groups[j]->at(k).id) - atom_ids.begin();
|
|
atomic_gradients[a] += coeff * cvcs[i]->atom_groups[j]->at(k).grad;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
if (tasks[task_system_force]) {
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Calculating system force of colvar \""+this->name+"\".\n");
|
|
|
|
ft.reset();
|
|
|
|
if(!tasks[task_extended_lagrangian] && (cvm::step_relative() > 0)) {
|
|
// get from the cvcs the system forces from the PREVIOUS step
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
(cvcs[i])->calc_force_invgrads();
|
|
// linear combination is assumed
|
|
cvm::increase_depth();
|
|
ft += (cvcs[i])->system_force() / ((cvcs[i])->sup_coeff * cvm::real (cvcs.size()));
|
|
cvm::decrease_depth();
|
|
}
|
|
}
|
|
|
|
if (tasks[task_report_Jacobian_force]) {
|
|
// 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;
|
|
}
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Done calculating system force of colvar \""+this->name+"\".\n");
|
|
}
|
|
|
|
if (tasks[task_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 (tasks[task_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;
|
|
}
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Done calculating colvar \""+this->name+"\".\n");
|
|
}
|
|
|
|
|
|
cvm::real colvar::update()
|
|
{
|
|
if (cvm::debug())
|
|
cvm::log ("Updating colvar \""+this->name+"\".\n");
|
|
|
|
|
|
// set to zero the applied force
|
|
f.reset();
|
|
|
|
// add the biases' force, which at this point should already have
|
|
// been summed over each bias using this colvar
|
|
f += fb;
|
|
|
|
|
|
if (tasks[task_lower_wall] || tasks[task_upper_wall]) {
|
|
|
|
// wall force
|
|
colvarvalue fw (this->type());
|
|
|
|
// if the two walls are applied concurrently, decide which is the
|
|
// closer one (on a periodic colvar, both walls may be applicable
|
|
// at the same time)
|
|
if ( (!tasks[task_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;
|
|
if (cvm::debug())
|
|
cvm::log ("Applying a lower wall force ("+
|
|
cvm::to_str (fw)+") to \""+this->name+"\".\n");
|
|
f += fw;
|
|
|
|
}
|
|
|
|
} else {
|
|
|
|
cvm::real const grad = this->dist2_lgrad (x, upper_wall);
|
|
if (grad > 0.0) {
|
|
fw = -0.5 * upper_wall_k * grad;
|
|
if (cvm::debug())
|
|
cvm::log ("Applying an upper wall force ("+
|
|
cvm::to_str (fw)+") to \""+this->name+"\".\n");
|
|
f += fw;
|
|
}
|
|
}
|
|
}
|
|
|
|
if (tasks[task_Jacobian_force]) {
|
|
|
|
cvm::increase_depth();
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
(cvcs[i])->calc_Jacobian_derivative();
|
|
}
|
|
cvm::decrease_depth();
|
|
|
|
fj.reset();
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
// linear combination is assumed
|
|
fj += 1.0 / ( cvm::real (cvcs.size()) * cvm::real ((cvcs[i])->sup_coeff) ) *
|
|
(cvcs[i])->Jacobian_derivative();
|
|
}
|
|
fj *= cvm::boltzmann() * cvm::temperature();
|
|
|
|
// the instantaneous Jacobian force was not included in the reported system force;
|
|
// instead, it is subtracted from the applied force (silent Jacobian correction)
|
|
if (! tasks[task_report_Jacobian_force])
|
|
f -= fj;
|
|
}
|
|
|
|
|
|
if (tasks[task_extended_lagrangian]) {
|
|
|
|
cvm::real dt = cvm::dt();
|
|
|
|
// the total force is applied to the fictitious mass, while the
|
|
// atoms only feel the harmonic force
|
|
// fr: extended coordinate force; f: colvar force applied to atomic coordinates
|
|
fr = f;
|
|
fr += (-0.5 * ext_force_k) * this->dist2_lgrad (xr, x);
|
|
f = (-0.5 * ext_force_k) * this->dist2_rgrad (xr, x);
|
|
|
|
// leap frog: starting from x_i, f_i, v_(i-1/2)
|
|
vr += (0.5 * dt) * fr / 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 (tasks[task_langevin]) {
|
|
vr -= dt * ext_gamma * vr.real_value;
|
|
vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
|
|
}
|
|
vr += (0.5 * dt) * fr / ext_mass;
|
|
xr += dt * vr;
|
|
xr.apply_constraints();
|
|
if (this->b_periodic) this->wrap (xr);
|
|
}
|
|
|
|
|
|
if (tasks[task_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()
|
|
{
|
|
if (cvm::debug())
|
|
cvm::log ("Communicating forces from colvar \""+this->name+"\".\n");
|
|
|
|
if (x.type() == colvarvalue::type_scalar) {
|
|
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
cvm::increase_depth();
|
|
(cvcs[i])->apply_force (f * (cvcs[i])->sup_coeff *
|
|
cvm::real ((cvcs[i])->sup_np) *
|
|
(std::pow ((cvcs[i])->value().real_value,
|
|
(cvcs[i])->sup_np-1)) );
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
} else {
|
|
|
|
for (size_t i = 0; i < cvcs.size(); i++) {
|
|
cvm::increase_depth();
|
|
(cvcs[i])->apply_force (f * (cvcs[i])->sup_coeff);
|
|
cvm::decrease_depth();
|
|
}
|
|
}
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Done communicating forces from colvar \""+this->name+"\".\n");
|
|
}
|
|
|
|
|
|
|
|
// ******************** METRIC FUNCTIONS ********************
|
|
// Use the metrics defined by \link cvc \endlink objects
|
|
|
|
|
|
bool colvar::periodic_boundaries (colvarvalue const &lb, colvarvalue const &ub) const
|
|
{
|
|
if ( (!tasks[task_lower_boundary]) || (!tasks[task_upper_boundary]) ) {
|
|
cvm::fatal_error ("Error: requesting to histogram the "
|
|
"collective variable \""+this->name+"\", but a "
|
|
"pair of lower and upper boundaries must be "
|
|
"defined.\n");
|
|
}
|
|
|
|
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 ( (!tasks[task_lower_boundary]) || (!tasks[task_upper_boundary]) ) {
|
|
cvm::fatal_error ("Error: requesting to histogram the "
|
|
"collective variable \""+this->name+"\", but a "
|
|
"pair of lower and upper boundaries must be "
|
|
"defined.\n");
|
|
}
|
|
|
|
return periodic_boundaries (lower_boundary, upper_boundary);
|
|
}
|
|
|
|
|
|
cvm::real colvar::dist2 (colvarvalue const &x1,
|
|
colvarvalue const &x2) const
|
|
{
|
|
return (cvcs[0])->dist2 (x1, x2);
|
|
}
|
|
|
|
colvarvalue colvar::dist2_lgrad (colvarvalue const &x1,
|
|
colvarvalue const &x2) const
|
|
{
|
|
return (cvcs[0])->dist2_lgrad (x1, x2);
|
|
}
|
|
|
|
colvarvalue colvar::dist2_rgrad (colvarvalue const &x1,
|
|
colvarvalue const &x2) const
|
|
{
|
|
return (cvcs[0])->dist2_rgrad (x1, x2);
|
|
}
|
|
|
|
cvm::real colvar::compare (colvarvalue const &x1,
|
|
colvarvalue const &x2) const
|
|
{
|
|
return (cvcs[0])->compare (x1, x2);
|
|
}
|
|
|
|
void colvar::wrap (colvarvalue &x) const
|
|
{
|
|
(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::fatal_error ("Error: the state file does not match the "
|
|
"configuration file, at colvar \""+name+"\".\n");
|
|
}
|
|
if (check_name.size() == 0) {
|
|
cvm::fatal_error ("Error: Collective variable in the "
|
|
"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 (tasks[colvar::task_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");
|
|
}
|
|
}
|
|
|
|
if (tasks[task_extended_lagrangian]) {
|
|
x_reported = xr;
|
|
} else {
|
|
x_reported = x;
|
|
}
|
|
|
|
if (tasks[task_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 (tasks[task_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 (tasks[task_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 (tasks[task_extended_lagrangian]) {
|
|
is >> xr;
|
|
x_reported = xr;
|
|
} else {
|
|
x_reported = x;
|
|
}
|
|
}
|
|
|
|
if (tasks[task_output_velocity]) {
|
|
|
|
is >> v_fdiff;
|
|
|
|
if (tasks[task_extended_lagrangian]) {
|
|
is >> vr;
|
|
v_reported = vr;
|
|
} else {
|
|
v_reported = v_fdiff;
|
|
}
|
|
}
|
|
|
|
if (tasks[task_output_system_force]) {
|
|
|
|
is >> ft;
|
|
|
|
if (tasks[task_extended_lagrangian]) {
|
|
is >> fr;
|
|
ft_reported = fr;
|
|
} else {
|
|
ft_reported = ft;
|
|
}
|
|
}
|
|
|
|
if (tasks[task_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 (tasks[task_output_velocity]) {
|
|
os << " v "
|
|
<< std::setprecision (cvm::cv_prec)
|
|
<< std::setw (cvm::cv_width)
|
|
<< v_reported << "\n";
|
|
}
|
|
|
|
if (tasks[task_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 (tasks[task_output_value]) {
|
|
|
|
os << " "
|
|
<< cvm::wrap_string (this->name, this_cv_width);
|
|
|
|
if (tasks[task_extended_lagrangian]) {
|
|
// restraint center
|
|
os << " r_"
|
|
<< cvm::wrap_string (this->name, this_cv_width-2);
|
|
}
|
|
}
|
|
|
|
if (tasks[task_output_velocity]) {
|
|
|
|
os << " v_"
|
|
<< cvm::wrap_string (this->name, this_cv_width-2);
|
|
|
|
if (tasks[task_extended_lagrangian]) {
|
|
// restraint center
|
|
os << " vr_"
|
|
<< cvm::wrap_string (this->name, this_cv_width-3);
|
|
}
|
|
}
|
|
|
|
if (tasks[task_output_energy]) {
|
|
os << " Ep_"
|
|
<< cvm::wrap_string (this->name, this_cv_width-3)
|
|
<< " Ek_"
|
|
<< cvm::wrap_string (this->name, this_cv_width-3);
|
|
}
|
|
|
|
if (tasks[task_output_system_force]) {
|
|
|
|
os << " fs_"
|
|
<< cvm::wrap_string (this->name, this_cv_width-2);
|
|
|
|
if (tasks[task_extended_lagrangian]) {
|
|
// restraint center
|
|
os << " fr_"
|
|
<< cvm::wrap_string (this->name, this_cv_width-3);
|
|
}
|
|
}
|
|
|
|
if (tasks[task_output_applied_force]) {
|
|
os << " fa_"
|
|
<< cvm::wrap_string (this->name, this_cv_width-2);
|
|
}
|
|
|
|
return os;
|
|
}
|
|
|
|
|
|
std::ostream & colvar::write_traj (std::ostream &os)
|
|
{
|
|
os << " ";
|
|
|
|
if (tasks[task_output_value]) {
|
|
|
|
if (tasks[task_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 (tasks[task_output_velocity]) {
|
|
|
|
if (tasks[task_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 (tasks[task_output_energy]) {
|
|
os << " "
|
|
<< std::setprecision (cvm::cv_prec) << std::setw (cvm::cv_width)
|
|
<< potential_energy
|
|
<< " "
|
|
<< kinetic_energy;
|
|
}
|
|
|
|
|
|
if (tasks[task_output_system_force]) {
|
|
|
|
if (tasks[task_extended_lagrangian]) {
|
|
os << " "
|
|
<< std::setprecision (cvm::cv_prec) << std::setw (cvm::cv_width)
|
|
<< ft;
|
|
}
|
|
|
|
os << " "
|
|
<< std::setprecision (cvm::cv_prec) << std::setw (cvm::cv_width)
|
|
<< ft_reported;
|
|
}
|
|
|
|
if (tasks[task_output_applied_force]) {
|
|
os << " "
|
|
<< std::setprecision (cvm::cv_prec) << std::setw (cvm::cv_width)
|
|
<< f;
|
|
}
|
|
|
|
return os;
|
|
}
|
|
|
|
void colvar::write_output_files()
|
|
{
|
|
if (cvm::b_analysis) {
|
|
|
|
if (acf.size()) {
|
|
cvm::log ("Writing acf to file \""+acf_outfile+"\".\n");
|
|
|
|
std::ofstream acf_os (acf_outfile.c_str());
|
|
if (! acf_os.good())
|
|
cvm::fatal_error ("Cannot open file \""+acf_outfile+"\".\n");
|
|
write_acf (acf_os);
|
|
acf_os.close();
|
|
}
|
|
|
|
if (runave_os.good()) {
|
|
runave_os.close();
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
|
|
// ******************** ANALYSIS FUNCTIONS ********************
|
|
|
|
void colvar::analyse()
|
|
{
|
|
if (tasks[task_runave]) {
|
|
calc_runave();
|
|
}
|
|
|
|
if (tasks[task_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();
|
|
}
|
|
|
|
|
|
void 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.size() || acf_v_history.size()) ) {
|
|
|
|
// first-step operations
|
|
|
|
colvar *cfcv = (acf_colvar_name.size() ?
|
|
cvm::colvar_p (acf_colvar_name) :
|
|
this);
|
|
if (cfcv->type() != this->type())
|
|
cvm::fatal_error ("Error: correlation function between \""+cfcv->name+
|
|
"\" and \""+this->name+"\" cannot be calculated, "
|
|
"because their value types are different.\n");
|
|
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);
|
|
|
|
switch (acf_type) {
|
|
|
|
case acf_vel:
|
|
// allocate space for the velocities history
|
|
for (size_t 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 (size_t 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_p (acf_colvar_name) :
|
|
this);
|
|
|
|
switch (acf_type) {
|
|
|
|
case acf_vel:
|
|
|
|
if (tasks[task_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 (tasks[task_fdiff_velocity]) {
|
|
// set it for the next step
|
|
x_old = x;
|
|
}
|
|
}
|
|
|
|
|
|
void 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();
|
|
|
|
// 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++;
|
|
}
|
|
}
|
|
|
|
|
|
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.size()) {
|
|
|
|
runave.type (x.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;
|
|
for (std::list<colvarvalue>::iterator 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 (std::list<colvarvalue>::iterator 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);
|
|
}
|
|
}
|
|
|
|
}
|
|
|
|
|