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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13207 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-03-09 14:50:53 +00:00
parent 08e77a79b3
commit 5a0a8f1335
11 changed files with 118 additions and 61 deletions
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31
lib/colvars/colvar.cpp
View File

@ -11,6 +11,7 @@
colvar::colvar(std::string const &conf)
: colvarparse(conf)
{
size_t i, j;
cvm::log("Initializing a new collective variable.\n");
@ -151,6 +152,7 @@ colvar::colvar(std::string const &conf)
cvm::error("Error: no valid components were provided "
"for this collective variable.\n",
INPUT_ERROR);
return;
}
cvm::log("All components initialized.\n");
@ -232,7 +234,6 @@ colvar::colvar(std::string const &conf)
x.type(cvc_value);
x_reported.type(cvc_value);
}
// If using scripted biases, any colvar may receive bias forces
// and will need its gradient
if (cvm::scripted_forces()) {
@ -319,6 +320,10 @@ colvar::colvar(std::string const &conf)
}
}
// at this point, the colvar's type is defined
f.type(value());
fb.type(value());
get_keyval(conf, "width", width, 1.0);
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
@ -374,10 +379,10 @@ colvar::colvar(std::string const &conf)
if (tasks[task_lower_wall] && tasks[task_upper_wall]) {
if (lower_wall >= upper_wall) {
cvm::error("Error: the upper wall, "+
cvm::to_str(upper_wall)+
", is not higher than the lower wall, "+
cvm::to_str(lower_wall)+".\n",
INPUT_ERROR);
cvm::to_str(upper_wall)+
", is not higher than the lower wall, "+
cvm::to_str(lower_wall)+".\n",
INPUT_ERROR);
}
if (dist2(lower_wall, upper_wall) < 1.0E-12) {
@ -391,15 +396,15 @@ colvar::colvar(std::string const &conf)
get_keyval(conf, "expandBoundaries", expand_boundaries, false);
if (expand_boundaries && periodic_boundaries()) {
cvm::error("Error: trying to expand boundaries that already "
"cover a whole period of a periodic colvar.\n",
INPUT_ERROR);
"cover a whole period of a periodic colvar.\n",
INPUT_ERROR);
}
if (expand_boundaries && hard_lower_boundary && hard_upper_boundary) {
cvm::error("Error: inconsistent configuration "
"(trying to expand boundaries with both "
"hardLowerBoundary and hardUpperBoundary enabled).\n",
INPUT_ERROR);
}
"(trying to expand boundaries with both "
"hardLowerBoundary and hardUpperBoundary enabled).\n",
INPUT_ERROR);
}
{
bool b_extended_lagrangian;
@ -722,11 +727,7 @@ int colvar::enable(colvar::task const &t)
case task_langevin:
case task_output_energy:
case task_scripted:
break;
case task_gradients:
f.type(value());
fb.type(value());
break;
case task_collect_gradients:

2
lib/colvars/colvarbias.cpp
View File

@ -6,7 +6,7 @@
colvarbias::colvarbias(std::string const &conf, char const *key)
: colvarparse(), has_data(false)
: colvarparse(conf), bias_energy(0.), has_data(false)
{
cvm::log("Initializing a new \""+std::string(key)+"\" instance.\n");

16
lib/colvars/colvarbias_abf.cpp
View File

@ -190,13 +190,6 @@ cvm::real colvarbias_abf::update()
// initialization stuff (file operations relying on n_abf_biases
// compute current value of colvars
if ( cvm::n_abf_biases == 1 && cvm::n_meta_biases == 0 ) {
// This is the only ABF bias
output_prefix = cvm::output_prefix;
} else {
output_prefix = cvm::output_prefix + "." + this->name;
}
for (size_t i=0; i<colvars.size(); i++) {
bin[i] = samples->current_bin_scalar(i);
}
@ -260,10 +253,19 @@ cvm::real colvarbias_abf::update()
}
}
// update the output prefix; TODO: move later to setup_output() function
if ( cvm::n_abf_biases == 1 && cvm::n_meta_biases == 0 ) {
// This is the only ABF bias
output_prefix = cvm::output_prefix;
} else {
output_prefix = cvm::output_prefix + "." + this->name;
}
if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
if (cvm::debug()) cvm::log("ABF bias trying to write gradients and samples to disk");
write_gradients_samples(output_prefix);
}
if (b_history_files && (cvm::step_absolute() % history_freq) == 0) {
cvm::log("ABFHISTORYFILE "+cvm::to_str(cvm::step_absolute()));
// file already exists iff cvm::step_relative() > 0

3
lib/colvars/colvarbias_restraint.cpp
View File

@ -153,8 +153,7 @@ cvm::real colvarbias_restraint::energy_difference(std::string const &conf)
}
if (get_keyval(conf, "centers", alt_colvar_centers, colvar_centers)) {
for (i = 0; i < colvars.size(); i++) {
colvar_centers[i].type(colvars[i]->value());
colvar_centers[i].apply_constraints();
alt_colvar_centers[i].apply_constraints();
}
}

18
lib/colvars/colvarmodule.cpp
View File

@ -41,7 +41,10 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
colvarmodule::use_scripted_forces = false;
colvarmodule::b_analysis = false;
colvarmodule::debug_gradients_step_size = 1.0e-07;
colvarmodule::rotation::monitor_crossings = false;
colvarmodule::rotation::crossing_threshold = 1.0e-02;
colvarmodule::cv_traj_freq = 100;
@ -52,7 +55,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
}
int colvarmodule::config_file(char const *config_filename)
int colvarmodule::read_config_file(char const *config_filename)
{
cvm::log(cvm::line_marker);
cvm::log("Reading new configuration from file \""+
@ -75,11 +78,11 @@ int colvarmodule::config_file(char const *config_filename)
}
config_s.close();
return config(conf);
return parse_config(conf);
}
int colvarmodule::config_string(std::string const &config_str)
int colvarmodule::read_config_string(std::string const &config_str)
{
cvm::log(cvm::line_marker);
cvm::log("Reading new configuration:\n");
@ -91,10 +94,10 @@ int colvarmodule::config_string(std::string const &config_str)
while (colvarparse::getline_nocomments(config_s, line)) {
conf.append(line+"\n");
}
return config(conf);
return parse_config(conf);
}
int colvarmodule::config(std::string &conf)
int colvarmodule::parse_config(std::string &conf)
{
int error_code = 0;
@ -156,6 +159,10 @@ int colvarmodule::parse_global_params(std::string const &conf)
debug_gradients_step_size,
colvarparse::parse_silent);
parse->get_keyval(conf, "monitorEigenvalueCrossing",
colvarmodule::rotation::monitor_crossings,
colvarmodule::rotation::monitor_crossings,
colvarparse::parse_silent);
parse->get_keyval(conf, "eigenvalueCrossingThreshold",
colvarmodule::rotation::crossing_threshold,
colvarmodule::rotation::crossing_threshold,
@ -1196,7 +1203,6 @@ size_t colvarmodule::restart_out_freq = 0;
size_t colvarmodule::cv_traj_freq = 0;
size_t colvarmodule::depth = 0;
bool colvarmodule::b_analysis = false;
cvm::real colvarmodule::rotation::crossing_threshold = 1.0E-04;
std::list<std::string> colvarmodule::index_group_names;
std::list<std::vector<int> > colvarmodule::index_groups;
bool colvarmodule::use_scripted_forces = false;

8
lib/colvars/colvarmodule.h
View File

@ -4,7 +4,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2015-02-04"
#define COLVARS_VERSION "2015-02-27"
#endif
#ifndef COLVARS_DEBUG
@ -200,14 +200,14 @@ public:
int reset();
/// Open a config file, load its contents, and pass it to config_string()
int config_file(char const *config_file_name);
int read_config_file(char const *config_file_name);
/// \brief Parse a config string assuming it is a complete configuration
/// (i.e. calling all parse functions)
int config_string(std::string const &conf);
int read_config_string(std::string const &conf);
/// \brief Parse a "clean" config string (no comments)
int config(std::string &conf);
int parse_config(std::string &conf);
// Parse functions (setup internal data based on a string)

13
lib/colvars/colvarparse.h
View File

@ -48,12 +48,25 @@ protected:
/// \brief Remove all the values from the config string
void strip_values(std::string &conf);
/// \brief Configuration string of the object
std::string config_string;
public:
inline colvarparse()
: save_delimiters(true)
{}
/// Constructor that stores the object's config string
inline colvarparse(const std::string& conf)
: save_delimiters(true), config_string(conf)
{}
inline const std::string& get_config()
{
return config_string;
}
/// How a keyword is parsed in a string
enum Parse_Mode {
/// \brief(default) Read the first instance of a keyword (if

42
lib/colvars/colvarscript.cpp
View File

@ -32,6 +32,7 @@ Managing the colvars module:\n\
config <string> -- read configuration from the given string\n\
reset -- delete all internal configuration\n\
delete -- delete this colvars module instance\n\
version -- return version of colvars code\n\
\n\
Input and output:\n\
list -- return a list of all variables\n\
@ -49,15 +50,18 @@ Input and output:\n\
result += "\n\
Accessing collective variables:\n\
colvar <name> value -- return the current value of the colvar <name>\n\
colvar <name> update -- recalculate the colvar <name>\n\
colvar <name> delete -- delete the colvar <name>\n\
colvar <name> addforce <F> -- apply given force on <name>\n\
colvar <name> value -- return the current value of colvar <name>\n\
colvar <name> update -- recalculate colvar <name>\n\
colvar <name> type -- return the type of colvar <name>\n\
colvar <name> delete -- delete colvar <name>\n\
colvar <name> addforce <F> -- apply given force on colvar <name>\n\
colvar <name> getconfig -- return config string of colvar <name>\n\
\n\
Accessing biases:\n\
bias <name> energy -- return the current energy of the bias <name>\n\
bias <name> update -- recalculate the bias <name>\n\
bias <name> delete -- delete the bias <name>\n\
bias <name> energy -- return the current energy of bias <name>\n\
bias <name> update -- recalculate bias <name>\n\
bias <name> delete -- delete bias <name>\n\
bias <name> getconfig -- return config string of bias <name>\n\
\n\
";
return COLVARSCRIPT_OK;
@ -73,6 +77,11 @@ Accessing biases:\n\
return proc_bias(argc-1, &(argv[1]));
}
if (cmd == "version") {
result = COLVARS_VERSION;
return COLVARSCRIPT_OK;
}
if (cmd == "reset") {
/// Delete every child object
colvars->reset();
@ -119,7 +128,7 @@ Accessing biases:\n\
result = "Missing arguments";
return COLVARSCRIPT_ERROR;
}
if (colvars->config_file(argv[2]) == COLVARS_OK) {
if (colvars->read_config_file(argv[2]) == COLVARS_OK) {
return COLVARSCRIPT_OK;
} else {
return COLVARSCRIPT_ERROR;
@ -133,7 +142,7 @@ Accessing biases:\n\
return COLVARSCRIPT_ERROR;
}
std::string conf = argv[2];
if (colvars->config_string(conf) == COLVARS_OK) {
if (colvars->read_config_string(conf) == COLVARS_OK) {
return COLVARSCRIPT_OK;
} else {
return COLVARSCRIPT_ERROR;
@ -221,6 +230,11 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
return COLVARSCRIPT_OK;
}
if (subcmd == "type") {
result = cv->value().type_desc(cv->value().value_type);
return COLVARSCRIPT_OK;
}
if (subcmd == "update") {
cv->calc();
cv->update();
@ -240,6 +254,11 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
return COLVARSCRIPT_OK;
}
if (subcmd == "getconfig") {
result = cv->get_config();
return COLVARSCRIPT_OK;
}
if (subcmd == "addforce") {
if (argc < 4) {
result = "addforce: missing parameter: force value";
@ -290,6 +309,11 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
return COLVARSCRIPT_OK;
}
if (subcmd == "getconfig") {
result = b->get_config();
return COLVARSCRIPT_OK;
}
// Subcommands for MW ABF
if (subcmd == "bin") {
int r = b->current_bin();

18
lib/colvars/colvartypes.cpp
View File

@ -8,6 +8,10 @@
#include "colvarparse.h"
bool colvarmodule::rotation::monitor_crossings = false;
cvm::real colvarmodule::rotation::crossing_threshold = 1.0E-02;
std::string cvm::rvector::to_simple_string() const
{
std::ostringstream os;
@ -329,14 +333,16 @@ void colvarmodule::rotation::calc_optimal_rotation(std::vector<cvm::atom_pos> co
lambda = L0;
q = Q0;
if (q_old.norm2() > 0.0) {
q.match(q_old);
if (q_old.inner(q) < (1.0 - crossing_threshold)) {
cvm::log("Warning: one molecular orientation has changed by more than "+
cvm::to_str(crossing_threshold)+": discontinuous rotation ?\n");
if (cvm::rotation::monitor_crossings) {
if (q_old.norm2() > 0.0) {
q.match(q_old);
if (q_old.inner(q) < (1.0 - crossing_threshold)) {
cvm::log("Warning: one molecular orientation has changed by more than "+
cvm::to_str(crossing_threshold)+": discontinuous rotation ?\n");
}
}
q_old = q;
}
q_old = q;
if (cvm::debug()) {
if (b_debug_gradients) {

2
lib/colvars/colvartypes.h
View File

@ -1531,6 +1531,8 @@ public:
}
}
/// \brief Whether to test for eigenvalue crossing
static bool monitor_crossings;
/// \brief Threshold for the eigenvalue crossing test
static cvm::real crossing_threshold;

26
lib/colvars/colvarvalue.h
View File

@ -171,27 +171,31 @@ public:
/// Set the type explicitly
inline void type(Type const &vti)
{
// reset the value based on the previous type
reset();
if ((value_type == type_vector) && (vti != type_vector)) {
vector1d_value.resize(0);
if (vti != value_type) {
// reset the value based on the previous type
reset();
if ((value_type == type_vector) && (vti != type_vector)) {
vector1d_value.resize(0);
}
value_type = vti;
}
value_type = vti;
}
/// Set the type after another \link colvarvalue \endlink
inline void type(colvarvalue const &x)
{
// reset the value held from based on the previous type
reset();
if (x.type() == type_vector) {
vector1d_value.resize(x.vector1d_value.size());
} else {
if (x.type() != value_type) {
// reset the value based on the previous type
reset();
if (value_type == type_vector) {
vector1d_value.resize(0);
}
value_type = x.type();
}
if (x.type() == type_vector) {
vector1d_value.resize(x.vector1d_value.size());
}
value_type = x.type();
}
/// Make the type a derivative of the original type