git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13445 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
226
lib/colvars/colvarbias_histogram.cpp
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226
lib/colvars/colvarbias_histogram.cpp
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/// -*- c++ -*-
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#include "colvarmodule.h"
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#include "colvar.h"
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#include "colvarbias_histogram.h"
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/// Histogram "bias" constructor
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colvarbias_histogram::colvarbias_histogram(std::string const &conf, char const *key)
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: colvarbias(conf, key),
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grid(NULL), out_name("")
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{
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get_keyval(conf, "outputFile", out_name, std::string(""));
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get_keyval(conf, "outputFreq", output_freq, cvm::restart_out_freq);
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/// with VMD, this may not be an error
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// if ( output_freq == 0 ) {
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// cvm::error("User required histogram with zero output frequency");
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// }
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colvar_array_size = 0;
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{
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size_t i;
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bool colvar_array = false;
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get_keyval(conf, "gatherVectorColvars", colvar_array, colvar_array);
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if (colvar_array) {
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for (i = 0; i < colvars.size(); i++) { // should be all vector
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if (colvars[i]->value().type() != colvarvalue::type_vector) {
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cvm::error("Error: used gatherVectorColvars with non-vector colvar.\n", INPUT_ERROR);
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return;
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}
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if (i == 0) {
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colvar_array_size = colvars[i]->value().size();
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if (colvar_array_size < 1) {
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cvm::error("Error: vector variable has dimension less than one.\n", INPUT_ERROR);
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return;
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}
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} else {
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if (colvar_array_size != colvars[i]->value().size()) {
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cvm::error("Error: trying to combine vector colvars of different lengths.\n", INPUT_ERROR);
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return;
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}
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}
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}
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} else {
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for (i = 0; i < colvars.size(); i++) { // should be all scalar
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if (colvars[i]->value().type() != colvarvalue::type_scalar) {
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cvm::error("Error: only scalar colvars are supported when gatherVectorColvars is off.\n", INPUT_ERROR);
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return;
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}
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}
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}
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}
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if (colvar_array_size > 0) {
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weights.assign(colvar_array_size, 1.0);
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get_keyval(conf, "weights", weights, weights, colvarparse::parse_silent);
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}
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grid = new colvar_grid_scalar();
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{
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std::string grid_conf;
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if (key_lookup(conf, "grid", grid_conf)) {
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grid->parse_params(grid_conf);
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} else {
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grid->init_from_colvars(colvars);
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}
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}
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cvm::log("Finished histogram setup.\n");
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}
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/// Destructor
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colvarbias_histogram::~colvarbias_histogram()
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{
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if (grid_os.is_open())
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grid_os.close();
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if (grid) {
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delete grid;
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grid = NULL;
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}
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if (cvm::n_histo_biases > 0)
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cvm::n_histo_biases -= 1;
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}
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/// Update the grid
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cvm::real colvarbias_histogram::update()
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{
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if (cvm::debug()) {
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cvm::log("Updating histogram bias " + this->name);
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}
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// assign a valid bin size
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bin.assign(colvars.size(), 0);
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if (out_name.size() == 0) {
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// At the first timestep, we need to assign out_name since
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// output_prefix is unset during the constructor
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if (cvm::step_relative() == 0) {
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out_name = cvm::output_prefix + "." + this->name + ".dat";
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cvm::log("Histogram " + this->name + " will be written to file \"" + out_name + "\"");
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}
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}
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if (colvar_array_size == 0) {
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// update indices for scalar values
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size_t i;
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for (i = 0; i < colvars.size(); i++) {
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bin[i] = grid->value_to_bin_scalar(colvars[i]->value(), i);
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}
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if (grid->index_ok(bin)) {
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grid->acc_value(bin, 1.0);
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}
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} else {
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// update indices for vector/array values
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size_t iv, i;
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for (iv = 0; iv < colvar_array_size; iv++) {
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for (i = 0; i < colvars.size(); i++) {
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bin[i] = grid->value_to_bin_scalar(colvars[i]->value().vector1d_value[iv], i);
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}
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if (grid->index_ok(bin)) {
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grid->acc_value(bin, weights[iv]);
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}
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}
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}
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if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
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write_output_files();
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}
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return 0.0; // no bias energy for histogram
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}
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int colvarbias_histogram::write_output_files()
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{
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if (out_name.size()) {
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cvm::log("Writing the histogram file \""+out_name+"\".\n");
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grid_os.open(out_name.c_str());
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if (!grid_os.is_open()) {
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cvm::error("Error opening histogram file " + out_name + " for writing");
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}
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// TODO add return code here
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grid->write_multicol(grid_os);
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grid_os.close();
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}
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return COLVARS_OK;
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}
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std::istream & colvarbias_histogram::read_restart(std::istream& is)
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{
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size_t const start_pos = is.tellg();
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cvm::log("Restarting collective variable histogram \""+
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this->name+"\".\n");
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std::string key, brace, conf;
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if ( !(is >> key) || !(key == "histogram") ||
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!(is >> brace) || !(brace == "{") ||
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!(is >> colvarparse::read_block("configuration", conf)) ) {
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cvm::log("Error: in reading restart configuration for histogram \""+
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this->name+"\" at position "+
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cvm::to_str(is.tellg())+" in stream.\n");
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is.clear();
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is.seekg(start_pos, std::ios::beg);
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is.setstate(std::ios::failbit);
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return is;
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}
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int id = -1;
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std::string name = "";
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if ( (colvarparse::get_keyval(conf, "name", name, std::string(""), colvarparse::parse_silent)) &&
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(name != this->name) )
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cvm::error("Error: in the restart file, the "
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"\"histogram\" block has a wrong name: different system?\n");
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if ( (id == -1) && (name == "") ) {
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cvm::error("Error: \"histogram\" block in the restart file "
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"has no name.\n");
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}
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if ( !(is >> key) || !(key == "grid")) {
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cvm::error("Error: in reading restart configuration for histogram \""+
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this->name+"\" at position "+
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cvm::to_str(is.tellg())+" in stream.\n");
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is.clear();
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is.seekg(start_pos, std::ios::beg);
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is.setstate(std::ios::failbit);
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return is;
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}
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if (! grid->read_raw(is)) {
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is.clear();
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is.seekg(start_pos, std::ios::beg);
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is.setstate(std::ios::failbit);
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return is;
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}
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is >> brace;
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if (brace != "}") {
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cvm::error("Error: corrupt restart information for ABF bias \""+
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this->name+"\": no matching brace at position "+
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cvm::to_str(is.tellg())+" in the restart file.\n");
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is.setstate(std::ios::failbit);
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}
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return is;
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}
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std::ostream & colvarbias_histogram::write_restart(std::ostream& os)
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{
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os << "histogram {\n"
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<< " configuration {\n"
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<< " name " << this->name << "\n";
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os << " }\n";
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os << "grid\n";
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grid->write_raw(os, 8);
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os << "}\n\n";
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return os;
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}
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