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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12610 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-10-07 20:30:09 +00:00
parent b14e621ecd
commit c59d3e6559
2 changed files with 45 additions and 19 deletions
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47
src/USER-COLVARS/colvarproxy_lammps.cpp
View File

@ -32,7 +32,7 @@
// local helper functions
// safely move filename to filename.extension
static void my_backup_file(const char *filename, const char *extension)
static int my_backup_file(const char *filename, const char *extension)
{
struct stat sbuf;
if (stat(filename, &sbuf) == 0) {
@ -48,9 +48,12 @@ static void my_backup_file(const char *filename, const char *extension)
if ( !sys_err_msg ) sys_err_msg = (char *) "(unknown error)";
fprintf(stderr,"Error renaming file %s to %s: %s\n",
filename, backup, sys_err_msg);
delete [] backup;
return COLVARS_ERROR;
}
delete [] backup;
}
return COLVARS_OK;
}
////////////////////////////////////////////////////////////////////////
@ -74,6 +77,10 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
do_exit=false;
restart_every=0;
// User-scripted forces are not available in LAMMPS
force_script_defined = false;
have_scripts = false;
// set input restart name and strip the extension, if present
input_prefix_str = std::string(inp_name ? inp_name : "");
if (input_prefix_str.rfind(".colvars.state") != std::string::npos)
@ -85,6 +92,12 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
// not so for restarts
restart_prefix_str = std::string("rest");
// check if it is possible to save output configuration
if ((!output_prefix_str.size()) && (!restart_output_prefix_str.size())) {
fatal_error ("Error: neither the final output state file or "
"the output restart file could be defined, exiting.\n");
}
// try to extract a restart prefix from a potential restart command.
LAMMPS_NS::Output *outp = _lmp->output;
if ((outp->restart_every_single > 0) && (outp->restart1 != 0)) {
@ -101,7 +114,12 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
void colvarproxy_lammps::init(const char *conf_file)
{
// create the colvarmodule instance
colvars = new colvarmodule(conf_file,this);
colvars = new colvarmodule (this);
// TODO move one or more of these to setup() if needed
colvars->config_file (conf_file);
colvars->setup_input();
colvars->setup_output();
if (_lmp->update->ntimestep != 0) {
cvm::log ("Initializing step number as firstTimestep.\n");
@ -245,6 +263,12 @@ void colvarproxy_lammps::log(std::string const &message)
}
}
void colvarproxy_lammps::error(std::string const &message)
{
// In LAMMPS, all errors are fatal
fatal_error(message);
}
void colvarproxy_lammps::fatal_error(std::string const &message)
{
log(message);
@ -311,33 +335,34 @@ e_pdb_field pdb_field_str2enum(std::string const &pdb_field_str)
return pdb_field;
}
void colvarproxy_lammps::load_coords(char const *pdb_filename,
int colvarproxy_lammps::load_coords(char const *pdb_filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const pdb_field_str,
std::string const &pdb_field_str,
double const pdb_field_value)
{
cvm::fatal_error("Reading collective variable coordinates "
"from a PDB file is currently not supported.\n");
"from a PDB file is currently not supported.\n");
return COLVARS_ERROR;
}
void colvarproxy_lammps::load_atoms(char const *pdb_filename,
int colvarproxy_lammps::load_atoms(char const *pdb_filename,
std::vector<cvm::atom> &atoms,
std::string const pdb_field_str,
std::string const &pdb_field_str,
double const pdb_field_value)
{
cvm::fatal_error("Selecting collective variable atoms "
"from a PDB file is currently not supported.\n");
return COLVARS_ERROR;
}
void colvarproxy_lammps::backup_file(char const *filename)
int colvarproxy_lammps::backup_file(char const *filename)
{
if (std::string(filename).rfind(std::string(".colvars.state"))
!= std::string::npos) {
my_backup_file(filename, ".old");
return my_backup_file(filename, ".old");
} else {
my_backup_file(filename, ".BAK");
return my_backup_file(filename, ".BAK");
}
}

17
src/USER-COLVARS/colvarproxy_lammps.h
View File

@ -110,9 +110,10 @@ class colvarproxy_lammps : public colvarproxy {
void add_energy (cvm::real energy) { bias_energy = energy; };
void request_system_force (bool yesno) { system_force_requested = yesno; };
void log (std::string const &message);
void fatal_error (std::string const &message);
void exit (std::string const &message);
void log(std::string const &message);
void error(std::string const &message);
void fatal_error(std::string const &message);
void exit(std::string const &message);
cvm::rvector position_distance (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2);
@ -121,18 +122,18 @@ class colvarproxy_lammps : public colvarproxy {
void select_closest_image (cvm::atom_pos &pos,
cvm::atom_pos const &ref_pos);
void load_atoms(char const *filename,
int load_atoms(char const *filename,
std::vector<cvm::atom> &atoms,
std::string const pdb_field,
std::string const &pdb_field,
double const pdb_field_value = 0.0);
void load_coords(char const *filename,
int load_coords(char const *filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const pdb_field,
std::string const &pdb_field,
double const pdb_field_value = 0.0);
void backup_file(char const *filename);
int backup_file(char const *filename);
cvm::real rand_gaussian(void) { return _random->gaussian(); };