Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/lib/colvars/colvarbias_histogram.cpp
2fcd26f6c41blammps-icms

Last Change
Raw File

colvarbias_histogram.cpp
View Options

// -*- c++ -*-
#include "colvarmodule.h"
#include "colvar.h"
#include "colvarbias_histogram.h"
/// Histogram "bias" constructor
colvarbias_histogram::colvarbias_histogram(std::string const &conf, char const *key)
: colvarbias(conf, key),
grid(NULL), out_name("")
{
size_t i;
get_keyval(conf, "outputFile", out_name, std::string(""));
get_keyval(conf, "outputFileDX", out_name_dx, std::string(""));
get_keyval(conf, "outputFreq", output_freq, cvm::restart_out_freq);
/// with VMD, this may not be an error
// if ( output_freq == 0 ) {
// cvm::error("User required histogram with zero output frequency");
// }
colvar_array_size = 0;
{
bool colvar_array = false;
get_keyval(conf, "gatherVectorColvars", colvar_array, colvar_array);
if (colvar_array) {
for (i = 0; i < colvars.size(); i++) { // should be all vector
if (colvars[i]->value().type() != colvarvalue::type_vector) {
cvm::error("Error: used gatherVectorColvars with non-vector colvar.\n", INPUT_ERROR);
return;
}
if (i == 0) {
colvar_array_size = colvars[i]->value().size();
if (colvar_array_size < 1) {
cvm::error("Error: vector variable has dimension less than one.\n", INPUT_ERROR);
return;
}
} else {
if (colvar_array_size != colvars[i]->value().size()) {
cvm::error("Error: trying to combine vector colvars of different lengths.\n", INPUT_ERROR);
return;
}
}
}
} else {
for (i = 0; i < colvars.size(); i++) { // should be all scalar
if (colvars[i]->value().type() != colvarvalue::type_scalar) {
cvm::error("Error: only scalar colvars are supported when gatherVectorColvars is off.\n", INPUT_ERROR);
return;
}
}
}
}
if (colvar_array_size > 0) {
weights.assign(colvar_array_size, 1.0);
get_keyval(conf, "weights", weights, weights, colvarparse::parse_silent);
}
for (i = 0; i < colvars.size(); i++) {
colvars[i]->enable(f_cv_grid);
}
grid = new colvar_grid_scalar();
{
std::string grid_conf;
if (key_lookup(conf, "grid", grid_conf)) {
grid->parse_params(grid_conf);
} else {
grid->init_from_colvars(colvars);
}
}
cvm::log("Finished histogram setup.\n");
}
/// Destructor
colvarbias_histogram::~colvarbias_histogram()
{
if (grid) {
delete grid;
grid = NULL;
}
if (cvm::n_histo_biases > 0)
cvm::n_histo_biases -= 1;
}
/// Update the grid
int colvarbias_histogram::update()
{
int error_code = COLVARS_OK;
// update base class
cvm::combine_errors(error_code, colvarbias::update());
if (cvm::debug()) {
cvm::log("Updating histogram bias " + this->name);
}
// assign a valid bin size
bin.assign(colvars.size(), 0);
if (out_name.size() == 0) {
// At the first timestep, we need to assign out_name since
// output_prefix is unset during the constructor
if (cvm::step_relative() == 0) {
out_name = cvm::output_prefix + "." + this->name + ".dat";
cvm::log("Histogram " + this->name + " will be written to file \"" + out_name + "\"");
}
}
if (out_name_dx.size() == 0) {
if (cvm::step_relative() == 0) {
out_name_dx = cvm::output_prefix + "." + this->name + ".dx";
cvm::log("Histogram " + this->name + " will be written to file \"" + out_name_dx + "\"");
}
}
if (colvar_array_size == 0) {
// update indices for scalar values
size_t i;
for (i = 0; i < colvars.size(); i++) {
bin[i] = grid->value_to_bin_scalar(colvars[i]->value(), i);
}
if (grid->index_ok(bin)) {
grid->acc_value(bin, 1.0);
}
} else {
// update indices for vector/array values
size_t iv, i;
for (iv = 0; iv < colvar_array_size; iv++) {
for (i = 0; i < colvars.size(); i++) {
bin[i] = grid->value_to_bin_scalar(colvars[i]->value().vector1d_value[iv], i);
}
if (grid->index_ok(bin)) {
grid->acc_value(bin, weights[iv]);
}
}
}
if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
write_output_files();
}
cvm::combine_errors(error_code, cvm::get_error());
return error_code;
}
int colvarbias_histogram::write_output_files()
{
if (!has_data) {
// nothing to write
return COLVARS_OK;
}
if (out_name.size()) {
cvm::log("Writing the histogram file \""+out_name+"\".\n");
cvm::backup_file(out_name.c_str());
cvm::ofstream grid_os(out_name.c_str());
if (!grid_os.is_open()) {
cvm::error("Error opening histogram file " + out_name + " for writing.\n", FILE_ERROR);
}
// TODO add return code here
grid->write_multicol(grid_os);
grid_os.close();
}
if (out_name_dx.size()) {
cvm::log("Writing the histogram file \""+out_name_dx+"\".\n");
cvm::backup_file(out_name_dx.c_str());
cvm::ofstream grid_os(out_name_dx.c_str());
if (!grid_os.is_open()) {
cvm::error("Error opening histogram file " + out_name_dx + " for writing.\n", FILE_ERROR);
}
// TODO add return code here
grid->write_opendx(grid_os);
grid_os.close();
}
return COLVARS_OK;
}
std::istream & colvarbias_histogram::read_restart(std::istream& is)
{
size_t const start_pos = is.tellg();
cvm::log("Restarting collective variable histogram \""+
this->name+"\".\n");
std::string key, brace, conf;
if ( !(is >> key) || !(key == "histogram") ||
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block("configuration", conf)) ) {
cvm::log("Error: in reading restart configuration for histogram \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
int id = -1;
std::string name = "";
if ( (colvarparse::get_keyval(conf, "name", name, std::string(""), colvarparse::parse_silent)) &&
(name != this->name) )
cvm::error("Error: in the restart file, the "
"\"histogram\" block has a wrong name: different system?\n");
if ( (id == -1) && (name == "") ) {
cvm::error("Error: \"histogram\" block in the restart file "
"has no name.\n");
}
if ( !(is >> key) || !(key == "grid")) {
cvm::error("Error: in reading restart configuration for histogram \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
if (! grid->read_raw(is)) {
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
is >> brace;
if (brace != "}") {
cvm::error("Error: corrupt restart information for ABF bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str(is.tellg())+" in the restart file.\n");
is.setstate(std::ios::failbit);
}
return is;
}
std::ostream & colvarbias_histogram::write_restart(std::ostream& os)
{
os << "histogram {\n"
<< " configuration {\n"
<< " name " << this->name << "\n";
os << " }\n";
os << "grid\n";
grid->write_raw(os, 8);
os << "}\n\n";
return os;
}
c4science · Help