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Update Colvars to version 2017-10-11

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Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
This commit is contained in:
Giacomo Fiorin
2017-10-13 13:25:02 -04:00
parent a973c65d67
commit 3e89b270fd
34 changed files with 1795 additions and 275 deletions
Download Patch File Download Diff File Expand all files Collapse all files

44
lib/colvars/colvarscript.cpp
View File

@ -11,7 +11,10 @@
#include <stdlib.h>
#include <string.h>
#define COLVARSCRIPT_CPP
#include "colvarscript.h"
#undef COLVARSCRIPT_CPP
#include "colvarproxy.h"
#include "colvardeps.h"
@ -21,6 +24,11 @@ colvarscript::colvarscript(colvarproxy *p)
colvars(p->colvars),
proxy_error(0)
{
comm_help.resize(colvarscript::cv_n_commands);
comm_fns.resize(colvarscript::cv_n_commands);
#define COLVARSCRIPT_INIT_FN
#include "colvarscript.h"
#undef COLVARSCRIPT_INIT_FN
}
@ -66,8 +74,7 @@ int colvarscript::run(int objc, unsigned char *const objv[])
}
if (objc < 2) {
result = help_string();
return COLVARS_OK;
return exec_command(cv_help, NULL, objc, objv);
}
std::string const cmd(obj_to_str(objv[1]));
@ -167,17 +174,7 @@ int colvarscript::run(int objc, unsigned char *const objv[])
/// Parse config from string
if (cmd == "config") {
if (objc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string const conf(obj_to_str(objv[2]));
if (colvars->read_config_string(conf) == COLVARS_OK) {
return COLVARS_OK;
} else {
result = "Error parsing configuration string";
return COLVARSCRIPT_ERROR;
}
return exec_command(cv_config, NULL, objc, objv);
}
/// Load an input state file
@ -204,6 +201,8 @@ int colvarscript::run(int objc, unsigned char *const objv[])
proxy->output_prefix() = obj_to_str(objv[2]);
int error = 0;
error |= colvars->setup_output();
error |= colvars->write_restart_file(colvars->output_prefix()+
".colvars.state");
error |= colvars->write_output_files();
return error ? COLVARSCRIPT_ERROR : COLVARS_OK;
}
@ -255,6 +254,10 @@ int colvarscript::run(int objc, unsigned char *const objv[])
}
}
if (cmd == "help") {
return exec_command(cv_help, NULL, objc, objv);
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
@ -295,7 +298,9 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
// 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));
if (colvars->cv_traj_os != NULL) {
colvars->write_traj_label(*(colvars->cv_traj_os));
}
return COLVARS_OK;
}
@ -374,7 +379,6 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
int colvarscript::proc_bias(colvarbias *b, int objc, unsigned char *const objv[]) {
std::string const key(obj_to_str(objv[0]));
std::string const subcmd(obj_to_str(objv[2]));
if (subcmd == "energy") {
@ -425,7 +429,9 @@ int colvarscript::proc_bias(colvarbias *b, int objc, unsigned char *const objv[]
// 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));
if (colvars->cv_traj_os != NULL) {
colvars->write_traj_label(*(colvars->cv_traj_os));
}
return COLVARS_OK;
}
@ -528,7 +534,7 @@ int colvarscript::proc_features(colvardeps *obj,
}
std::string colvarscript::help_string()
std::string colvarscript::help_string() const
{
std::string buf;
buf = "Usage: cv <subcommand> [args...]\n\
@ -538,7 +544,7 @@ 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\
version -- return version of Colvars code\n\
\n\
Input and output:\n\
list -- return a list of all variables\n\
@ -564,6 +570,8 @@ Accessing collective variables:\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> getappliedforce -- return applied force of colvar <name>\n\
colvar <name> gettotalforce -- return total force of colvar <name>\n\
colvar <name> getconfig -- return config string of colvar <name>\n\
colvar <name> cvcflags <fl> -- enable or disable cvcs according to 0/1 flags\n\
colvar <name> get <f> -- get the value of the colvar feature <f>\n\