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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12811 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-12-02 02:09:53 +00:00
parent 9c0f849594
commit c4af1cdbbd
34 changed files with 5927 additions and 4786 deletions
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107
lib/colvars/colvarscript.cpp
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@ -1,28 +1,31 @@
// -*- c++ -*-
#include <cstdlib>
#include <stdlib.h>
#include <string.h>
#include "colvarscript.h"
colvarscript::colvarscript (colvarproxy *p)
: proxy (p),
colvars (p->colvars),
proxy_error (0)
colvarscript::colvarscript(colvarproxy *p)
: proxy(p),
colvars(p->colvars),
proxy_error(0)
{
}
/// Run method based on given arguments
int colvarscript::run (int argc, char const *argv[]) {
int colvarscript::run(int argc, char const *argv[]) {
result = "";
if (cvm::debug()) {
cvm::log ("Called script run with " + cvm::to_str(argc) + " args");
for (int i = 0; i < argc; i++) { cvm::log (argv[i]); }
cvm::log("Called script run with " + cvm::to_str(argc) + " args");
for (int i = 0; i < argc; i++) { cvm::log(argv[i]); }
}
if (argc < 2) {
result = "usage: "+std::string (argv[0])+" <subcommand> [args...]\n\
result = "usage: "+std::string(argv[0])+" <subcommand> [args...]\n\
\n\
Managing the colvars module:\n\
configfile <file name> -- read configuration from a file\n\
@ -63,11 +66,11 @@ Accessing biases:\n\
std::string cmd = argv[1];
if (cmd == "colvar") {
return proc_colvar (argc-1, &(argv[1]));
return proc_colvar(argc-1, &(argv[1]));
}
if (cmd == "bias") {
return proc_bias (argc-1, &(argv[1]));
return proc_bias(argc-1, &(argv[1]));
}
if (cmd == "reset") {
@ -116,7 +119,7 @@ Accessing biases:\n\
result = "Missing arguments";
return COLVARSCRIPT_ERROR;
}
if (colvars->config_file (argv[2]) == COLVARS_OK) {
if (colvars->config_file(argv[2]) == COLVARS_OK) {
return COLVARSCRIPT_OK;
} else {
return COLVARSCRIPT_ERROR;
@ -130,7 +133,7 @@ Accessing biases:\n\
return COLVARSCRIPT_ERROR;
}
std::string conf = argv[2];
if (colvars->config_string (conf) == COLVARS_OK) {
if (colvars->config_string(conf) == COLVARS_OK) {
return COLVARSCRIPT_OK;
} else {
return COLVARSCRIPT_ERROR;
@ -156,13 +159,13 @@ Accessing biases:\n\
/// Print the values that would go on colvars.traj
if (cmd == "printframelabels") {
std::ostringstream os;
colvars->write_traj_label (os);
colvars->write_traj_label(os);
result = os.str();
return COLVARSCRIPT_OK;
}
if (cmd == "printframe") {
std::ostringstream os;
colvars->write_traj (os);
colvars->write_traj(os);
result = os.str();
return COLVARSCRIPT_OK;
}
@ -171,7 +174,7 @@ Accessing biases:\n\
if (argc == 2) {
int f = proxy->frame();
if (f >= 0) {
result = cvm::to_str (f);
result = cvm::to_str(f);
return COLVARSCRIPT_OK;
} else {
result = "Frame number is not available";
@ -182,7 +185,7 @@ Accessing biases:\n\
// returns the plain result to let scripts detect available frames
long int f = proxy->frame(strtol(argv[2], NULL, 10));
colvars->it = proxy->frame();
result = cvm::to_str (f);
result = cvm::to_str(f);
return COLVARSCRIPT_OK;
} else {
result = "Wrong arguments to command \"frame\"";
@ -195,9 +198,9 @@ Accessing biases:\n\
}
int colvarscript::proc_colvar (int argc, char const *argv[]) {
int colvarscript::proc_colvar(int argc, char const *argv[]) {
std::string name = argv[1];
colvar *cv = cvm::colvar_by_name (name);
colvar *cv = cvm::colvar_by_name(name);
if (cv == NULL) {
result = "Colvar not found: " + name;
return COLVARSCRIPT_ERROR;
@ -209,14 +212,19 @@ int colvarscript::proc_colvar (int argc, char const *argv[]) {
std::string subcmd = argv[2];
if (subcmd == "value") {
result = cvm::to_str(cv->value(), 0, cvm::cv_prec);
result = (cv->value()).to_simple_string();
return COLVARSCRIPT_OK;
}
if (subcmd == "width") {
result = cvm::to_str(cv->width, 0, cvm::cv_prec);
return COLVARSCRIPT_OK;
}
if (subcmd == "update") {
cv->calc();
cv->update();
result = cvm::to_str(cv->value(), 0, cvm::cv_prec);
result = (cv->value()).to_simple_string();
return COLVARSCRIPT_OK;
}
@ -228,27 +236,27 @@ int colvarscript::proc_colvar (int argc, char const *argv[]) {
// colvar destructor is tasked with the cleanup
delete cv;
// TODO this could be done by the destructors
colvars->write_traj_label (colvars->cv_traj_os);
colvars->write_traj_label(colvars->cv_traj_os);
return COLVARSCRIPT_OK;
}
if (subcmd == "addforce") {
if (argc < 4) {
result = "Missing parameter: force value";
result = "addforce: missing parameter: force value";
return COLVARSCRIPT_ERROR;
}
std::string f_str = argv[3];
std::istringstream is (f_str);
std::istringstream is(f_str);
is.width(cvm::cv_width);
is.precision(cvm::cv_prec);
colvarvalue force (cv->type());
colvarvalue force(cv->value());
force.is_derivative();
if (!(is >> force)) {
result = "Error parsing force value";
if (force.from_simple_string(is.str()) != COLVARS_OK) {
result = "addforce : error parsing force value";
return COLVARSCRIPT_ERROR;
}
cv->add_bias_force(force);
result = cvm::to_str(force, cvm::cv_width, cvm::cv_prec);
result = force.to_simple_string();
return COLVARSCRIPT_OK;
}
@ -257,9 +265,9 @@ int colvarscript::proc_colvar (int argc, char const *argv[]) {
}
int colvarscript::proc_bias (int argc, char const *argv[]) {
int colvarscript::proc_bias(int argc, char const *argv[]) {
std::string name = argv[1];
colvarbias *b = cvm::bias_by_name (name);
colvarbias *b = cvm::bias_by_name(name);
if (b == NULL) {
result = "Bias not found: " + name;
return COLVARSCRIPT_ERROR;
@ -282,16 +290,53 @@ int colvarscript::proc_bias (int argc, char const *argv[]) {
return COLVARSCRIPT_OK;
}
// Subcommands for MW ABF
if (subcmd == "bin") {
int r = b->current_bin();
result = cvm::to_str(r);
return COLVARSCRIPT_OK;
}
if (subcmd == "binnum") {
int r = b->bin_num();
if (r < 0) {
result = "Error: calling bin_num() for bias " + b->name;
return COLVARSCRIPT_ERROR;
}
result = cvm::to_str(r);
return COLVARSCRIPT_OK;
}
if (subcmd == "share") {
int r = b->replica_share();
if (r < 0) {
result = "Error: calling replica_share() for bias " + b->name;
return COLVARSCRIPT_ERROR;
}
result = cvm::to_str(r);
return COLVARSCRIPT_OK;
}
// End commands for MW ABF
if (subcmd == "delete") {
// the bias destructor takes care of the cleanup at cvm level
delete b;
// TODO this could be done by the destructors
colvars->write_traj_label (colvars->cv_traj_os);
colvars->write_traj_label(colvars->cv_traj_os);
return COLVARSCRIPT_OK;
}
if (argc >= 4) {
// std::string param = argv[3];
std::string param = argv[3];
if (subcmd == "count") {
int index;
if (!(std::istringstream(param) >> index)) {
result = "bin_count: error parsing bin index";
return COLVARSCRIPT_ERROR;
}
result = cvm::to_str(b->bin_count(index));
return COLVARSCRIPT_OK;
}
result = "Syntax error";
return COLVARSCRIPT_ERROR;