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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
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232
lib/colvars/colvarscript.h
View File

@ -8,21 +8,27 @@
// Colvars repository at GitHub.
#ifndef COLVARSCRIPT_H
#define COLVARSCRIPT_H
//#define COLVARSCRIPT_H // Delay definition until later
#include <string>
#include <vector>
#include <map>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarbias.h"
#include "colvarproxy.h"
// Only these error values are part of the scripting interface
#define COLVARSCRIPT_ERROR -1
#define COLVARSCRIPT_OK 0
class colvarscript {
private:
colvarproxy *proxy;
colvarmodule *colvars;
@ -35,16 +41,93 @@ public:
colvarscript(colvarproxy * p);
inline ~colvarscript() {}
/// If an error is caught by the proxy through fatal_error(), this is set to COLVARSCRIPT_ERROR
/// If an error is caught by the proxy through fatal_error(), this is set to
/// COLVARSCRIPT_ERROR
int proxy_error;
/// If an error is returned by one of the methods, it should set this to the error message
/// If an error is returned by one of the methods, it should set this to the
/// error message
std::string result;
/// Run script command with given positional arguments (objects)
int run(int objc, unsigned char *const objv[]);
/// Set the return value of the script command to the given string
inline void set_str_result(std::string const &s)
{
result = s;
}
/// Build and return a short help
std::string help_string(void) const;
/// Use scripting language to get the string representation of an object
inline char const *obj_to_str(unsigned char *const obj)
{
return cvm::proxy->script_obj_to_str(obj);
}
enum command {
cv_help,
cv_version,
cv_config,
cv_configfile,
cv_reset,
cv_delete,
cv_list,
cv_list_biases,
cv_load,
cv_save,
cv_update,
cv_addenergy,
cv_getenergy,
cv_printframe,
cv_printframelabels,
cv_frame,
cv_colvar,
cv_colvar_value,
cv_colvar_update,
cv_colvar_type,
cv_colvar_delete,
cv_colvar_addforce,
cv_colvar_getappliedforce,
cv_colvar_gettotalforce,
cv_colvar_cvcflags,
cv_colvar_getconfig,
cv_colvar_get,
cv_colvar_set,
cv_bias,
cv_bias_energy,
cv_bias_update,
cv_bias_delete,
cv_bias_getconfig,
cv_bias_get,
cv_bias_set,
cv_n_commands
};
/// Execute a script command
inline int exec_command(command c,
void *pobj,
int objc, unsigned char * const *objv)
{
return (*(comm_fns[c]))(pobj, objc, objv);
}
/// Get help for a command (TODO reformat for each language?)
inline std::string command_help(colvarscript::command c) const
{
return comm_help[c];
}
/// Clear all object results
inline void clear_results()
{
result.clear();
}
private:
/// Run subcommands on colvar
int proc_colvar(colvar *cv, int argc, unsigned char *const argv[]);
@ -55,17 +138,146 @@ private:
int proc_features(colvardeps *obj,
int argc, unsigned char *const argv[]);
/// Build and return a short help
std::string help_string(void);
/// Internal identifiers of command strings
std::map<std::string, command> comm_str_map;
public:
/// Help strings for each command
std::vector<std::string> comm_help;
inline char const *obj_to_str(unsigned char *const obj)
{
return cvm::proxy->script_obj_to_str(obj);
}
/// Number of arguments for each command
std::vector<size_t> comm_n_args;
/// Arguments for each command
std::vector< std::vector<std::string> > comm_args;
/// Implementations of each command
std::vector<int (*)(void *, int, unsigned char * const *)> comm_fns;
};
/// Get a pointer to the main colvarscript object
inline static colvarscript *colvarscript_obj()
{
return cvm::main()->proxy->script;
}
/// Get a pointer to the colvar object pointed to by pobj
inline static colvar *colvar_obj(void *pobj)
{
return reinterpret_cast<colvar *>(pobj);
}
/// Get a pointer to the colvarbias object pointed to by pobj
inline static colvarbias *colvarbias_obj(void *pobj)
{
return reinterpret_cast<colvarbias *>(pobj);
}
#define CVSCRIPT_COMM_FNAME(COMM) cvscript_ ## COMM
#define CVSCRIPT_COMM_PROTO(COMM) \
int CVSCRIPT_COMM_FNAME(COMM)(void *, int, unsigned char *const *);
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
CVSCRIPT_COMM_PROTO(COMM)
#undef COLVARSCRIPT_H
#endif // #ifndef COLVARSCRIPT_H
#ifdef COLVARSCRIPT_CPP
#define CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
int CVSCRIPT_COMM_FNAME(COMM)(void *pobj, \
int objc, unsigned char *const objv[]) \
{ \
colvarscript *script = colvarscript_obj(); \
script->clear_results(); \
if (objc < 2+N_ARGS_MIN) /* "cv" and "COMM" are 1st and 2nd */ { \
script->set_str_result("Missing arguments\n" + \
script->command_help(colvarscript::COMM)); \
return COLVARSCRIPT_ERROR; \
} \
if (objc > 2+N_ARGS_MAX) { \
script->set_str_result("Too many arguments\n" + \
script->command_help(colvarscript::COMM)); \
return COLVARSCRIPT_ERROR; \
} \
FN_BODY; \
}
#undef CVSCRIPT
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)
#endif // #ifdef COLVARSCRIPT_CPP
#ifdef COLVARSCRIPT_INIT_FN
#define CVSCRIPT_COMM_INIT(COMM,HELP,ARGS) { \
comm_str_map[#COMM] = COMM; \
comm_help[COMM] = HELP; \
comm_fns[COMM] = &(CVSCRIPT_COMM_FNAME(COMM)); \
}
#undef CVSCRIPT
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
CVSCRIPT_COMM_INIT(COMM,HELP,ARGS)
#endif
#if !defined(COLVARSCRIPT_H) || defined(COLVARSCRIPT_INIT_FN)
#define COLVARSCRIPT_H
#ifndef COLVARSCRIPT_INIT_FN
#ifdef __cplusplus
extern "C" {
#endif
#endif
// Add optional arguments for command-specific help?
CVSCRIPT(cv_help,
"Print the help message",
0, 0,
{},
script->set_str_result(script->help_string());
return COLVARS_OK;
)
CVSCRIPT(cv_config,
"Read configuration from the given string",
1, 1,
{ "conf (str) - Configuration string" },
std::string const conf(script->obj_to_str(objv[2]));
if (cvm::main()->read_config_string(conf) == COLVARS_OK) {
return COLVARS_OK;
}
script->set_str_result("Error parsing configuration string");
return COLVARSCRIPT_ERROR;
)
CVSCRIPT(cv_addenergy,
"Add an energy to the MD engine",
1, 1,
{ "E (float) - Amount of energy to add" },
cvm::main()->total_bias_energy +=
strtod(script->obj_to_str(objv[2]), NULL);
return COLVARS_OK;
)
CVSCRIPT(cv_getenergy,
"Get the current Colvars energy",
1, 1,
{ "E (float) - Store the energy in this variable" },
double *energy = reinterpret_cast<double *>(objv[2]);
*energy = cvm::main()->total_bias_energy;
return COLVARS_OK;
)
#ifndef COLVARSCRIPT_INIT_FN
#ifdef __cplusplus
} // extern "C"
#endif
#endif
#undef CVSCRIPT
#endif // #ifndef COLVARSCRIPT_H