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Update Colvars to version 2022-05-09

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This update includes one new feature (neural-network based collective
variables), several small enhancements (including an automatic definition of
grid boundaries for angle-based CVs, and a normalization option for
eigenvector-based CVs), bugfixes and documentation improvements.

Usage information for specific features included in the Colvars library
(i.e. not just the library as a whole) is now also reported to the screen or
LAMMPS logfile (as is done already in other LAMMPS classes).

Notable to LAMMPS code development are the removals of duplicated code and of
ambiguously-named preprocessor defines in the Colvars headers.  Since the
last PR, the existing regression tests have also been running automatically
via GitHub Actions.

The following pull requests in the Colvars repository are relevant to LAMMPS:

- 475 Remove fatal error condition
  https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin)

- 474 Allow normalizing eigenvector vector components to deal with unit change
  https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin)

- 470 Better error handling in the initialization of NeuralNetwork CV
  https://github.com/Colvars/colvars/pull/470 (@HanatoK)

- 468 Add examples of histogram configuration, with and without explicit grid parameters
  https://github.com/Colvars/colvars/pull/468 (@giacomofiorin)

- 464 Fix #463 using more fine-grained features
  https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin)

- 447 [RFC] New option "scaledBiasingForce" for colvarbias
  https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin)

- 444 [RFC] Implementation of dense neural network as CV
  https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin)

- 443 Fix explicit gradient dependency of sub-CVs
  https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin)

- 442 Persistent bias count
  https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin)

- 437 Return type of bias from scripting interface
  https://github.com/Colvars/colvars/pull/437 (@giacomofiorin)

- 434 More flexible use of boundaries from colvars by grids
  https://github.com/Colvars/colvars/pull/434 (@jhenin)

- 433 Prevent double-free in linearCombination
  https://github.com/Colvars/colvars/pull/433 (@HanatoK)

- 428 More complete documentation for index file format (NDX)
  https://github.com/Colvars/colvars/pull/428 (@giacomofiorin)

- 426 Integrate functional version of backup_file() into base proxy class
  https://github.com/Colvars/colvars/pull/426 (@giacomofiorin)

- 424 Track CVC inheritance when documenting feature usage
  https://github.com/Colvars/colvars/pull/424 (@giacomofiorin)

- 419 Generate citation report while running computations
  https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin)

- 415 Rebin metadynamics bias from explicit hills when available
  https://github.com/Colvars/colvars/pull/415 (@giacomofiorin)

- 312 Ignore a keyword if it has content to the left of it (regardless of braces)
  https://github.com/Colvars/colvars/pull/312 (@giacomofiorin)

Authors: @giacomofiorin, @HanatoK, @jhenin
This commit is contained in:
Giacomo Fiorin
2022-05-10 11:24:54 -04:00
parent 4737b9efb7
commit 1220bea011
66 changed files with 4040 additions and 1221 deletions
Download Patch File Download Diff File Expand all files Collapse all files

60
lib/colvars/colvarscript.cpp
View File

@ -11,13 +11,6 @@
#include <cstring>
#include <sstream>
#if defined(NAMD_TCL) || defined(VMDTCL)
#define COLVARS_TCL
#endif
#ifdef COLVARS_TCL
#include <tcl.h>
#endif
#include "colvarproxy.h"
#include "colvardeps.h"
#include "colvarscript.h"
@ -38,20 +31,25 @@ extern "C" int tcl_run_colvarscript_command(ClientData clientData,
#endif
colvarscript::colvarscript(colvarproxy *p)
colvarscript::colvarscript(colvarproxy *p, colvarmodule *m)
: proxy_(p),
colvars(p->colvars),
proxy_error(0)
colvars(m)
{
cmd_names = NULL;
init_commands();
#ifdef COLVARS_TCL
// must be called after constructing derived proxy class to allow for overloading
proxy()->init_tcl_pointers();
// TODO put this in backend functions so we don't have to delete
Tcl_Interp *interp = reinterpret_cast<Tcl_Interp *>(proxy_->get_tcl_interp());
Tcl_Interp *const interp = proxy()->get_tcl_interp();
if (interp == NULL) {
cvm::error("Error: trying to construct colvarscript without a Tcl interpreter.\n");
return;
}
Tcl_DeleteCommand(interp, "cv");
Tcl_CreateObjCommand(interp, "cv", tcl_run_colvarscript_command,
(ClientData) this, (Tcl_CmdDeleteProc *) NULL);
cvm::log("Redefining the Tcl \"cv\" command to the new script interface.");
cvm::log("Redefining the Tcl \"cv\" command to the new script interface.\n");
#endif
}
@ -136,7 +134,7 @@ int colvarscript::init_command(colvarscript::command const &comm,
for (int iarg = 0; iarg < n_args_max; iarg++) {
if (! std::getline(is, line)) {
return cvm::error("Error: could not initialize help string for scripting "
"command \""+std::string(name)+"\".\n", BUG_ERROR);
"command \""+std::string(name)+"\".\n", COLVARS_BUG_ERROR);
}
cmd_arghelp[comm].push_back(line);
}
@ -180,7 +178,7 @@ std::string colvarscript::get_cmd_prefix(colvarscript::Object_type t)
case use_bias:
return std::string("bias_"); break;
default:
cvm::error("Error: undefined colvarscript object type.", BUG_ERROR);
cvm::error("Error: undefined colvarscript object type.", COLVARS_BUG_ERROR);
return std::string("");
}
}
@ -194,7 +192,7 @@ char const *colvarscript::get_command_help(char const *cmd)
return cmd_help[c].c_str();
}
cvm::error("Error: command "+std::string(cmd)+
" is not implemented.\n", INPUT_ERROR);
" is not implemented.\n", COLVARS_INPUT_ERROR);
return NULL;
}
@ -206,7 +204,7 @@ char const *colvarscript::get_command_rethelp(char const *cmd)
return cmd_rethelp[c].c_str();
}
cvm::error("Error: command "+std::string(cmd)+
" is not implemented.\n", INPUT_ERROR);
" is not implemented.\n", COLVARS_INPUT_ERROR);
return NULL;
}
@ -218,7 +216,7 @@ char const *colvarscript::get_command_arghelp(char const *cmd, int i)
return cmd_arghelp[c][i].c_str();
}
cvm::error("Error: command "+std::string(cmd)+
" is not implemented.\n", INPUT_ERROR);
" is not implemented.\n", COLVARS_INPUT_ERROR);
return NULL;
}
@ -230,7 +228,7 @@ int colvarscript::get_command_n_args_min(char const *cmd)
return cmd_n_args_min[c];
}
cvm::error("Error: command "+std::string(cmd)+
" is not implemented.\n", INPUT_ERROR);
" is not implemented.\n", COLVARS_INPUT_ERROR);
return -1;
}
@ -242,7 +240,7 @@ int colvarscript::get_command_n_args_max(char const *cmd)
return cmd_n_args_max[c];
}
cvm::error("Error: command "+std::string(cmd)+
" is not implemented.\n", INPUT_ERROR);
" is not implemented.\n", COLVARS_INPUT_ERROR);
return -1;
}
@ -254,7 +252,7 @@ char const *colvarscript::get_command_full_help(char const *cmd)
return cmd_full_help[c].c_str();
}
cvm::error("Error: command "+std::string(cmd)+
" is not implemented.\n", INPUT_ERROR);
" is not implemented.\n", COLVARS_INPUT_ERROR);
return NULL;
}
@ -338,9 +336,8 @@ std::string colvarscript::get_command_cmdline_help(colvarscript::Object_type t,
return get_command_cmdline_syntax(t, c)+"\n\n"+
get_command_full_help(cmd_names[c]);
}
cvm::error("Error: could not find scripting command \""+cmd+"\".",
INPUT_ERROR);
return std::string("");
cvm::set_error_bits(COLVARS_INPUT_ERROR);
return std::string("Could not find scripting command \""+cmd+"\".");
}
@ -477,7 +474,7 @@ std::vector<std::string> colvarscript::obj_to_str_vector(unsigned char *obj)
i++;
if (i >= str.length()) {
cvm::error("Error: could not split the following string:\n"+
str+"\n", INPUT_ERROR);
str+"\n", COLVARS_INPUT_ERROR);
break;
}
new_result.push_back(std::string(""));
@ -485,7 +482,7 @@ std::vector<std::string> colvarscript::obj_to_str_vector(unsigned char *obj)
new_result.back().append(1, str[i]);
if (i >= str.length()) {
cvm::error("Error: could not split the following string:\n"+
str+"\n", INPUT_ERROR);
str+"\n", COLVARS_INPUT_ERROR);
break;
} else {
i++;
@ -616,7 +613,7 @@ int run_colvarscript_command(int objc, unsigned char *const objv[])
colvarscript *script = cv ? cv->proxy->script : NULL;
if (!script) {
cvm::error("Called run_colvarscript_command without a script object.\n",
BUG_ERROR);
COLVARS_BUG_ERROR);
return -1;
}
int retval = script->run(objc, objv);
@ -644,13 +641,13 @@ int tcl_colvars_vmd_init(Tcl_Interp *interp, int molid);
#endif
#if !defined(VMDTCL) && !defined(NAMD_TCL)
// Initialize Colvars when loaded as a shared library into Tcl interpreter
extern "C" {
int Colvars_Init(Tcl_Interp *interp) {
colvarproxy *proxy = new colvarproxy();
colvarmodule *colvars = new colvarmodule(proxy);
proxy->set_tcl_interp(reinterpret_cast<void *>(interp));
proxy->set_tcl_interp(interp);
proxy->colvars = colvars;
proxy->script = new colvarscript(proxy);
Tcl_CreateObjCommand(interp, "cv", tcl_run_colvarscript_command,
(ClientData *) NULL, (Tcl_CmdDeleteProc *) NULL);
Tcl_EvalEx(interp, "package provide colvars", -1, 0);
@ -715,8 +712,7 @@ extern "C" int tcl_run_colvarscript_command(ClientData /* clientData */,
}
colvarproxy *proxy = colvars->proxy;
Tcl_Interp *interp = my_interp ? my_interp :
reinterpret_cast<Tcl_Interp *>(proxy->get_tcl_interp());
Tcl_Interp *interp = my_interp ? my_interp : proxy->get_tcl_interp();
colvarscript *script = colvarscript_obj();
if (!script) {
char const *errstr = "Called tcl_run_colvarscript_command "
@ -744,8 +740,8 @@ extern "C" int tcl_run_colvarscript_command(ClientData /* clientData */,
Tcl_SetResult(interp, const_cast<char *>(result.c_str()),
TCL_VOLATILE);
if (proxy->delete_requested() || cvm::get_error_bit(FATAL_ERROR)) {
if (proxy->delete_requested() && !proxy->simulation_running()) {
if (proxy->delete_requested()) {
if (!proxy->simulation_running()) {
// Running in VMD
Tcl_SetResult(interp,
const_cast<char *>("Deleting Colvars module"