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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14004 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-09-08 23:38:11 +00:00
parent 11d819482c
commit 942cce877b
7 changed files with 80 additions and 127 deletions
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4
lib/colvars/Makefile.fermi
View File

@ -7,8 +7,8 @@ EXTRAMAKE = Makefile.lammps.empty
# ------ SETTINGS ------
CXX = g++
CXXFLAGS = -O2 -mpc64 -march=native -funroll-loops -g \
-fno-rtti -fno-exceptions -Wall -Wno-sign-compare # -DCOLVARS_DEBUG
CXXFLAGS = -O2 -mpc64 -g -fPIC \
-Wall -Wno-sign-compare # -DCOLVARS_DEBUG
ARCHIVE = ar
ARCHFLAG = -rscv
SHELL = /bin/sh

80
lib/colvars/colvar.cpp
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@ -9,11 +9,17 @@
#include <algorithm>
/// Compare two cvcs using their names
/// Used to sort CVC array in scripted coordinates
bool compare(colvar::cvc *i, colvar::cvc *j) {
return i->name < j->name;
}
colvar::colvar(std::string const &conf)
: colvarparse(conf)
{
size_t i, j;
size_t i;
cvm::log("Initializing a new collective variable.\n");
get_keyval(conf, "name", this->name,
@ -81,9 +87,12 @@ colvar::colvar(std::string const &conf)
return; \
} \
} \
if ( ! cvcs.back()->name.size()) \
cvcs.back()->name = std::string(def_config_key)+ \
(cvm::to_str(++def_count)); \
if ( ! cvcs.back()->name.size()){ \
std::ostringstream s; \
s << def_config_key << std::setfill('0') << std::setw(4) << ++def_count;\
cvcs.back()->name = s.str(); \
/* pad cvc number for correct ordering when sorting by name */\
} \
if (cvm::debug()) \
cvm::log("Done initializing a \""+ \
std::string(def_config_key)+ \
@ -193,27 +202,21 @@ colvar::colvar(std::string const &conf)
x.vector1d_value.resize(size);
}
// Sort array of cvcs based on values of componentExp
std::vector<cvc *> temp_vec;
for (i = 1; i <= cvcs.size(); i++) {
for (j = 0; j < cvcs.size(); j++) {
if (cvcs[j]->sup_np == int(i)) {
temp_vec.push_back(cvcs[j]);
break;
}
// Sort array of cvcs based on their names
// Note: default CVC names are in input order for same type of CVC
std::sort(cvcs.begin(), cvcs.end(), compare);
if(cvcs.size() > 1) {
cvm::log("Sorted list of components for this scripted colvar:");
for (i = 0; i < cvcs.size(); i++) {
cvm::log(cvm::to_str(i+1) + " " + cvcs[i]->name);
}
}
if (temp_vec.size() != cvcs.size()) {
cvm::error("Could not find order numbers for all components "
"in componentExp values.");
return;
}
cvcs = temp_vec;
// Build ordered list of component values that will be
// passed to the script
for (j = 0; j < cvcs.size(); j++) {
sorted_cvc_values.push_back(&(cvcs[j]->value()));
for (i = 0; i < cvcs.size(); i++) {
sorted_cvc_values.push_back(&(cvcs[i]->value()));
}
b_homogeneous = false;
@ -846,7 +849,22 @@ void colvar::calc()
if (cvm::debug())
cvm::log("Collecting data from atom groups.\n");
// Update the enabled/disabled status of cvcs if necessary
if (cvc_flags.size()) {
bool any = false;
for (i = 0; i < cvcs.size(); i++) {
cvcs[i]->b_enabled = cvc_flags[i];
any = any || cvc_flags[i];
}
if (!any) {
cvm::error("ERROR: All CVCs are disabled for colvar " + this->name +"\n");
return;
}
cvc_flags.resize(0);
}
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
atoms.reset_atoms_data();
@ -1101,9 +1119,9 @@ cvm::real colvar::update()
// 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)) ) {
(this->dist2(x_reported, lower_wall) < this->dist2(x_reported, upper_wall)) ) {
cvm::real const grad = this->dist2_lgrad(x, lower_wall);
cvm::real const grad = this->dist2_lgrad(x_reported, lower_wall);
if (grad < 0.0) {
fw = -0.5 * lower_wall_k * grad;
if (cvm::debug())
@ -1115,7 +1133,7 @@ cvm::real colvar::update()
} else {
cvm::real const grad = this->dist2_lgrad(x, upper_wall);
cvm::real const grad = this->dist2_lgrad(x_reported, upper_wall);
if (grad > 0.0) {
fw = -0.5 * upper_wall_k * grad;
if (cvm::debug())
@ -1220,12 +1238,13 @@ void colvar::communicate_forces()
return;
}
int grad_index = 0; // index in the scripted gradients, to account for some components being disabled
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
cvm::increase_depth();
// cvc force is colvar force times colvar/cvc Jacobian
// (vector-matrix product)
(cvcs[i])->apply_force(colvarvalue(f.as_vector() * func_grads[i],
(cvcs[i])->apply_force(colvarvalue(f.as_vector() * func_grads[grad_index++],
cvcs[i]->value().type()));
cvm::decrease_depth();
}
@ -1258,20 +1277,13 @@ void colvar::communicate_forces()
int colvar::set_cvc_flags(std::vector<bool> const &flags) {
size_t i;
if (flags.size() != cvcs.size()) {
cvm::error("ERROR: Wrong number of CVC flags provided.");
return COLVARS_ERROR;
}
bool e = false;
for (i = 0; i < cvcs.size(); i++) {
cvcs[i]->b_enabled = flags[i];
e = e || flags[i];
}
if (!e) {
cvm::error("ERROR: All CVCs are disabled for this colvar.");
return COLVARS_ERROR;
}
// We cannot enable or disable cvcs in the middle of a timestep or colvar evaluation sequence
// so we store the flags that will be enforced at the next call to calc()
cvc_flags = flags;
return COLVARS_OK;
}

3
lib/colvars/colvar.h
View File

@ -514,6 +514,9 @@ protected:
/// \brief Array of \link cvc \endlink objects
std::vector<cvc *> cvcs;
/// \brief Flags to enable or disable cvcs at next colvar evaluation
std::vector<bool> cvc_flags;
/// \brief Initialize the sorted list of atom IDs for atoms involved
/// in all cvcs (called when enabling task_collect_gradients)
void build_atom_list(void);

2
lib/colvars/colvarbias_histogram.cpp
View File

@ -155,6 +155,7 @@ int colvarbias_histogram::write_output_files()
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);
@ -166,6 +167,7 @@ int colvarbias_histogram::write_output_files()
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);

72
lib/colvars/colvargrid.cpp
View File

@ -24,31 +24,6 @@ colvar_grid_count::colvar_grid_count(std::vector<colvar *> &colvars,
: colvar_grid<size_t>(colvars, def_count, 1)
{}
std::istream & colvar_grid_count::read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, conf;
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
}
read_raw(is);
return is;
}
std::ostream & colvar_grid_count::write_restart(std::ostream &os)
{
write_params(os);
write_raw(os);
return os;
}
colvar_grid_scalar::colvar_grid_scalar()
: colvar_grid<cvm::real>(), samples(NULL), grad(NULL)
{}
@ -79,30 +54,6 @@ colvar_grid_scalar::~colvar_grid_scalar()
}
}
std::istream & colvar_grid_scalar::read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, conf;
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
}
read_raw(is);
return is;
}
std::ostream & colvar_grid_scalar::write_restart(std::ostream &os)
{
write_params(os);
write_raw(os);
return os;
}
cvm::real colvar_grid_scalar::maximum_value() const
{
cvm::real max = data[0];
@ -163,29 +114,6 @@ colvar_grid_gradient::colvar_grid_gradient(std::vector<colvar *> &colvars)
: colvar_grid<cvm::real>(colvars, 0.0, colvars.size()), samples(NULL)
{}
std::istream & colvar_grid_gradient::read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, conf;
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
}
read_raw(is);
return is;
}
std::ostream & colvar_grid_gradient::write_restart(std::ostream &os)
{
write_params(os);
write_raw(os);
return os;
}
void colvar_grid_gradient::write_1D_integral(std::ostream &os)
{
cvm::real bin, min, integral;

44
lib/colvars/colvargrid.h
View File

@ -836,6 +836,32 @@ public:
}
/// \brief Read grid entry in restart file
std::istream & read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, conf;
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
}
read_raw(is);
return is;
}
/// \brief Write grid entry in restart file
std::ostream & write_restart(std::ostream &os)
{
write_params(os);
write_raw(os);
return os;
}
/// \brief Write the grid data without labels, as they are
/// represented in memory
/// \param buf_size Number of values per line
@ -1106,12 +1132,6 @@ public:
return new_data[address(ix) + imult];
}
/// \brief Read the grid from a restart
std::istream & read_restart(std::istream &is);
/// \brief Write the grid to a restart
std::ostream & write_restart(std::ostream &os);
/// \brief Get the value from a formatted output and transform it
/// into the internal representation (it may have been rescaled or
/// manipulated)
@ -1240,12 +1260,6 @@ public:
has_data = true;
}
/// \brief Read the grid from a restart
std::istream & read_restart(std::istream &is);
/// \brief Write the grid to a restart
std::ostream & write_restart(std::ostream &os);
/// \brief Return the highest value
cvm::real maximum_value() const;
@ -1343,12 +1357,6 @@ public:
}
/// \brief Read the grid from a restart
std::istream & read_restart(std::istream &is);
/// \brief Write the grid to a restart
std::ostream & write_restart(std::ostream &os);
/// Compute and return average value for a 1D gradient grid
inline cvm::real average()
{

2
lib/colvars/colvarmodule.h
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@ -4,7 +4,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2015-07-21"
#define COLVARS_VERSION "2015-09-03"
#endif
#ifndef COLVARS_DEBUG