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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13126 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-02-19 18:20:52 +00:00
parent f300f2367e
commit 067833cf07
21 changed files with 597 additions and 360 deletions
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115
lib/colvars/colvarbias_abf.cpp
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@ -76,6 +76,8 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
if (!colvars[i]->tasks[colvar::task_extended_lagrangian]) {
// request computation of Jacobian force
// ultimately, will be done regardless of extended Lagrangian
// and colvar should then just report zero Jacobian force
colvars[i]->enable(colvar::task_Jacobian_force);
// request Jacobian force as part as system force
@ -116,7 +118,11 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
force = new cvm::real [colvars.size()];
// Construct empty grids based on the colvars
samples = new colvar_grid_count (colvars);
if (cvm::debug()) {
cvm::log("Allocating count and free energy gradient grids.\n");
}
samples = new colvar_grid_count(colvars);
gradients = new colvar_grid_gradient(colvars);
gradients->samples = samples;
samples->has_parent_data = true;
@ -124,7 +130,7 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
// For shared ABF, we store a second set of grids.
// This used to be only if "shared" was defined,
// but now we allow calling share externally (e.g. from Tcl).
last_samples = new colvar_grid_count (colvars);
last_samples = new colvar_grid_count(colvars);
last_gradients = new colvar_grid_gradient(colvars);
last_gradients->samples = last_samples;
last_samples->has_parent_data = true;
@ -260,9 +266,9 @@ cvm::real colvarbias_abf::update()
}
if (b_history_files && (cvm::step_absolute() % history_freq) == 0) {
cvm::log("ABFHISTORYFILE "+cvm::to_str(cvm::step_absolute()));
// append to existing file only if cvm::step_absolute() > 0
// file already exists iff cvm::step_relative() > 0
// otherwise, backup and replace
write_gradients_samples(output_prefix + ".hist", (cvm::step_absolute() > 0));
write_gradients_samples(output_prefix + ".hist", (cvm::step_relative() > 0));
}
if (shared_on && shared_last_step >= 0 && cvm::step_absolute() % shared_freq == 0) {
@ -365,28 +371,32 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
std::string gradients_out_name = prefix + ".grad";
std::ios::openmode mode = (append ? std::ios::app : std::ios::out);
std::ofstream samples_os;
std::ofstream gradients_os;
cvm::ofstream samples_os;
cvm::ofstream gradients_os;
if (!append) cvm::backup_file(samples_out_name.c_str());
samples_os.open(samples_out_name.c_str(), mode);
if (!samples_os.good()) cvm::error("Error opening ABF samples file " + samples_out_name + " for writing");
if (!samples_os.is_open()) {
cvm::error("Error opening ABF samples file " + samples_out_name + " for writing");
}
samples->write_multicol(samples_os);
samples_os.close();
if (!append) cvm::backup_file(gradients_out_name.c_str());
gradients_os.open(gradients_out_name.c_str(), mode);
if (!gradients_os.good()) cvm::error("Error opening ABF gradient file " + gradients_out_name + " for writing");
if (!gradients_os.is_open()) {
cvm::error("Error opening ABF gradient file " + gradients_out_name + " for writing");
}
gradients->write_multicol(gradients_os);
gradients_os.close();
if (colvars.size() == 1) {
std::string pmf_out_name = prefix + ".pmf";
if (!append) cvm::backup_file(pmf_out_name.c_str());
std::ofstream pmf_os;
cvm::ofstream pmf_os;
// Do numerical integration and output a PMF
pmf_os.open(pmf_out_name.c_str(), mode);
if (!pmf_os.good()) cvm::error("Error opening pmf file " + pmf_out_name + " for writing");
if (!pmf_os.is_open()) cvm::error("Error opening pmf file " + pmf_out_name + " for writing");
gradients->write_1D_integral(pmf_os);
pmf_os << std::endl;
pmf_os.close();
@ -428,13 +438,13 @@ void colvarbias_abf::read_gradients_samples()
cvm::log("Reading sample count from " + samples_in_name + " and gradients from " + gradients_in_name);
is.open(samples_in_name.c_str());
if (!is.good()) cvm::error("Error opening ABF samples file " + samples_in_name + " for reading");
if (!is.is_open()) cvm::error("Error opening ABF samples file " + samples_in_name + " for reading");
samples->read_multicol(is, true);
is.close();
is.clear();
is.open(gradients_in_name.c_str());
if (!is.good()) cvm::error("Error opening ABF gradient file " + gradients_in_name + " for reading");
if (!is.is_open()) cvm::error("Error opening ABF gradient file " + gradients_in_name + " for reading");
gradients->read_multicol(is, true);
is.close();
}
@ -550,13 +560,41 @@ colvarbias_histogram::colvarbias_histogram(std::string const &conf, char const *
: colvarbias(conf, key),
grid(NULL), out_name("")
{
get_keyval(conf, "outputfreq", output_freq, cvm::restart_out_freq);
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");
// }
if ( output_freq == 0 ) {
cvm::error("User required histogram with zero output frequency");
{
colvar_array_size = 1;
bool colvar_array = false;
if (get_keyval(conf, "sumVectorColvars", colvar_array, colvar_array)) {
size_t i;
for (i = 0; i < colvars.size(); i++) {
if (colvars[i]->value().type() == colvarvalue::type_vector) {
if (colvar_array_size == 1) {
colvar_array_size = colvars[i]->value().size();
} else {
if (colvar_array_size != colvars[i]->value().size()) {
cvm::error("Error: trying to combine vector colvars of different lengths.\n", INPUT_ERROR);
}
}
}
}
}
}
grid = new colvar_grid_count();
{
std::string grid_conf;
if (key_lookup(conf, "grid", grid_conf)) {
grid->parse_params(grid_conf);
} else {
grid->init_from_colvars(colvars);
}
}
grid = new colvar_grid_count (colvars);
bin.assign(colvars.size(), 0);
cvm::log("Finished histogram setup.\n");
@ -565,7 +603,8 @@ colvarbias_histogram::colvarbias_histogram(std::string const &conf, char const *
/// Destructor
colvarbias_histogram::~colvarbias_histogram()
{
if (grid_os.good()) grid_os.close();
if (grid_os.is_open())
grid_os.close();
if (grid) {
delete grid;
@ -579,7 +618,10 @@ colvarbias_histogram::~colvarbias_histogram()
/// Update the grid
cvm::real colvarbias_histogram::update()
{
if (cvm::debug()) cvm::log("Updating Grid bias " + this->name);
if (cvm::debug()) {
cvm::log("Updating histogram bias " + this->name);
}
// At the first timestep, we need to assign out_name since
// output_prefix is unset during the constructor
@ -589,22 +631,49 @@ cvm::real colvarbias_histogram::update()
cvm::log("Histogram " + this->name + " will be written to file \"" + out_name + "\"");
}
for (size_t i=0; i<colvars.size(); i++) {
bin[i] = grid->current_bin_scalar(i);
bin.assign(colvars.size(), 0);
{
// update indices for all scalar values
size_t i;
for (i = 0; i < colvars.size(); i++) {
if (colvars[i]->value().type() == colvarvalue::type_scalar) {
bin[i] = grid->value_to_bin_scalar(colvars[i]->value(), i);
}
}
}
if ( grid->index_ok(bin) ) { // Only within bounds of the grid...
grid->incr_count(bin);
if (colvar_array_size > 1) {
// update indices for all vector/array values
size_t iv, i;
for (iv = 0; iv < colvar_array_size; iv++) {
for (i = 0; i < colvars.size(); i++) {
if (colvars[i]->value().type() == colvarvalue::type_vector) {
bin[i] = grid->value_to_bin_scalar(colvars[i]->value().vector1d_value[iv], i);
}
}
if (grid->index_ok(bin)) {
// Only within bounds of the grid...
grid->incr_count(bin);
}
}
} else {
if (grid->index_ok(bin)) {
// Only within bounds of the grid...
grid->incr_count(bin);
}
}
if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
if (cvm::debug()) cvm::log("Histogram bias trying to write grid to disk");
grid_os.open(out_name.c_str());
if (!grid_os.good()) cvm::error("Error opening histogram file " + out_name + " for writing");
if (!grid_os.is_open()) cvm::error("Error opening histogram file " + out_name + " for writing");
grid->write_multicol(grid_os);
grid_os.close();
}
return 0.0; // no bias energy for histogram
}