ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update colvars library to the state of 16 Oct 2014

Browse Source
This commit is contained in:
Axel Kohlmeyer
2014-10-16 17:46:56 -04:00
parent 9d25e7e8ec
commit ac3359b2d6
12 changed files with 135 additions and 109 deletions
Download Patch File Download Diff File Expand all files Collapse all files

BIN
doc/PDF/colvars-refman-lammps.pdf
View File

Binary file not shown.

29
lib/colvars/colvar.cpp
View File

@ -53,11 +53,17 @@ colvar::colvar (std::string const &conf)
if (cvcp != NULL) { \
cvcs.push_back (cvcp); \
cvcp->check_keywords (def_conf, def_config_key); \
if (cvm::get_error()) { \
cvm::error("Error: in setting up component \"" \
def_config_key"\".\n"); \
return; \
} \
cvm::decrease_depth(); \
} else { \
cvm::error ("Error: in allocating component \"" \
cvm::error("Error: in allocating component \"" \
def_config_key"\".\n", \
MEMORY_ERROR); \
return; \
} \
if ( (cvcp->period != 0.0) || (cvcp->wrap_center != 0.0) ) { \
if ( (cvcp->function_type != std::string ("distance_z")) && \
@ -70,6 +76,7 @@ colvar::colvar (std::string const &conf)
"Period: "+cvm::to_str(cvcp->period) + \
" wrapAround: "+cvm::to_str(cvcp->wrap_center), \
INPUT_ERROR); \
return; \
} \
} \
if ( ! cvcs.back()->name.size()) \
@ -150,7 +157,7 @@ colvar::colvar (std::string const &conf)
"", colvarparse::parse_silent)) {
enable(task_scripted);
cvm::log("This colvar is a scripted function.");
cvm::log("This colvar uses scripted function \"" + scripted_function + "\".");
std::string type_str;
get_keyval (conf, "scriptedFunctionType", type_str, "scalar");
@ -187,18 +194,20 @@ colvar::colvar (std::string const &conf)
}
}
// this is set false if any of the components has an exponent
// different from 1 in the polynomial
b_linear = true;
// these will be set to false if any of the cvcs has them false
b_inverse_gradients = true;
b_Jacobian_force = true;
if (!tasks[task_scripted]) {
// this is set false if any of the components has an exponent
// different from 1 in the polynomial
b_linear = true;
// these will be set to false if any of the cvcs has them false
b_inverse_gradients = true;
b_Jacobian_force = true;
}
// Decide whether the colvar is periodic
// Used to wrap extended DOF if extendedLagrangian is on
if (cvcs.size() == 1 && (cvcs[0])->b_periodic && (cvcs[0])->sup_np == 1
&& (cvcs[0])->sup_coeff == 1.0 ) {
&& (cvcs[0])->sup_coeff == 1.0
&& !tasks[task_scripted]) {
this->b_periodic = true;
this->period = (cvcs[0])->period;
// TODO write explicit wrap() function for colvars to allow for

11
lib/colvars/colvaratoms.cpp
View File

@ -138,6 +138,7 @@ int cvm::atom_group::parse (std::string const &conf,
for (size_t i = 0; i < atom_indexes.size(); i++) {
this->push_back (cvm::atom (atom_indexes[i]));
}
if (cvm::get_error()) return COLVARS_ERROR;
} else {
cvm::error ("Error: no numbers provided for \""
"atomNumbers\".\n", INPUT_ERROR);
@ -166,6 +167,7 @@ int cvm::atom_group::parse (std::string const &conf,
for (size_t i = 0; i < index_groups_i->size(); i++) {
this->push_back (cvm::atom ((*index_groups_i)[i]));
}
if (cvm::get_error()) return COLVARS_ERROR;
}
}
@ -185,6 +187,7 @@ int cvm::atom_group::parse (std::string const &conf,
for (int anum = initial; anum <= final; anum++) {
this->push_back (cvm::atom (anum));
}
if (cvm::get_error()) return COLVARS_ERROR;
range_conf = "";
continue;
}
@ -235,6 +238,7 @@ int cvm::atom_group::parse (std::string const &conf,
for (int resid = initial; resid <= final; resid++) {
this->push_back (cvm::atom (resid, atom_name, psf_segid));
}
if (cvm::get_error()) return COLVARS_ERROR;
range_conf = "";
} else {
cvm::error ("Error: cannot parse definition for \""
@ -272,6 +276,9 @@ int cvm::atom_group::parse (std::string const &conf,
}
}
// Catch any errors from all the initialization steps above
if (cvm::get_error()) return COLVARS_ERROR;
for (std::vector<cvm::atom>::iterator a1 = this->begin();
a1 != this->end(); ++a1) {
std::vector<cvm::atom>::iterator a2 = a1;
@ -433,6 +440,10 @@ int cvm::atom_group::parse (std::string const &conf,
std::string (key)+"\".\n");
this->check_keywords (group_conf, key);
if (cvm::get_error()) {
cvm::error("Error setting up atom group \""+std::string (key)+"\".");
return COLVARS_ERROR;
}
cvm::log ("Atom group \""+std::string (key)+"\" defined, "+
cvm::to_str (this->size())+" atoms initialized: total mass = "+

13
lib/colvars/colvarcomp.cpp
View File

@ -47,11 +47,16 @@ void colvar::cvc::parse_group (std::string const &conf,
bool optional)
{
if (key_lookup (conf, group_key)) {
group.parse (conf, group_key);
if (group.parse (conf, group_key) != COLVARS_OK) {
cvm::error ("Error parsing definition for atom group \""+
std::string (group_key)+"\".\n");
return;
}
} else {
if (! optional) {
cvm::fatal_error ("Error: definition for atom group \""+
cvm::error ("Error: definition for atom group \""+
std::string (group_key)+"\" not found.\n");
return;
}
}
}
@ -137,9 +142,7 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
21, 14)+"\n");
cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
cvm::to_str (std::fabs (x_1 - x_0 - dx_pred) /
std::fabs (x_1 - x_0),
12, 5)+
".\n");
std::fabs (x_1 - x_0), 12, 5)+"\n");
}
}

15
lib/colvars/colvarcomp_distances.cpp
View File

@ -725,7 +725,7 @@ colvar::rmsd::rmsd (std::string const &conf)
return;
}
if (atoms.ref_pos_group != NULL) {
if (atoms.ref_pos_group != NULL && b_Jacobian_derivative) {
cvm::log ("The option \"refPositionsGroup\" (alternative group for fitting) was enabled: "
"Jacobian derivatives of the RMSD will not be calculated.\n");
b_Jacobian_derivative = false;
@ -788,10 +788,21 @@ colvar::rmsd::rmsd (std::string const &conf)
atoms.ref_pos = ref_pos;
atoms.center_ref_pos();
cvm::log ("This is a standard minimum RMSD, derivatives of the optimal rotation "
"will not be computed as they cancel out in the gradients.");
atoms.b_fit_gradients = false;
}
if (atoms.b_rotate) {
// TODO: finer-grained control of this would require exposing a
// "request_Jacobian_derivative()" method to the colvar, and the same
// from the colvar to biases
// TODO: this should not be enabled here anyway, as it is not specific of the
// component - instead it should be decided in a generic way by the atom group
// request the calculation of the derivatives of the rotation defined by the atom group
atoms.rot.request_group1_gradients (atoms.size());
// request derivatives of optimal rotation wrt reference coordinates for Jacobian:
// this is only required for ABF, but we do both groups here for better caching
atoms.rot.request_group2_gradients (atoms.size());
}
}

98
lib/colvars/colvarmodule.cpp
View File

@ -99,7 +99,7 @@ int colvarmodule::config (std::string &conf)
// parse global options
error_code |= parse_global_params (conf);
if (error_code != COLVARS_OK) {
if (error_code != COLVARS_OK || cvm::get_error()) {
set_error_bits(INPUT_ERROR);
return COLVARS_ERROR;
}
@ -107,13 +107,23 @@ int colvarmodule::config (std::string &conf)
// parse the options for collective variables
error_code |= parse_colvars (conf);
if (error_code != COLVARS_OK || cvm::get_error()) {
set_error_bits(INPUT_ERROR);
return COLVARS_ERROR;
}
// parse the options for biases
error_code |= parse_biases (conf);
if (error_code != COLVARS_OK || cvm::get_error()) {
set_error_bits(INPUT_ERROR);
return COLVARS_ERROR;
}
// done parsing known keywords, check that all keywords found were valid ones
error_code |= parse->check_keywords (conf, "colvarmodule");
if (error_code != COLVARS_OK) {
if (error_code != COLVARS_OK || cvm::get_error()) {
set_error_bits(INPUT_ERROR);
return COLVARS_ERROR;
}
@ -179,12 +189,11 @@ int colvarmodule::parse_colvars (std::string const &conf)
cvm::log (cvm::line_marker);
cvm::increase_depth();
colvars.push_back (new colvar (colvar_conf));
if (cvm::get_error()) {
delete colvars.back();
colvars.pop_back();
return COLVARS_ERROR;
}
if ((colvars.back())->check_keywords (colvar_conf, "colvar") != COLVARS_OK) {
if (cvm::get_error() ||
((colvars.back())->check_keywords (colvar_conf, "colvar") != COLVARS_OK)) {
cvm::log("Error while constructing colvar number " +
cvm::to_str(colvars.size()) + " : deleting.");
delete colvars.back(); // the colvar destructor updates the colvars array
return COLVARS_ERROR;
}
cvm::decrease_depth();
@ -192,6 +201,7 @@ int colvarmodule::parse_colvars (std::string const &conf)
cvm::error("Error: \"colvar\" keyword found without any configuration.\n", INPUT_ERROR);
return COLVARS_ERROR;
}
cvm::decrease_depth();
colvar_conf = "";
}
@ -208,6 +218,17 @@ int colvarmodule::parse_colvars (std::string const &conf)
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
bool colvarmodule::check_new_bias(std::string &conf, char const *key)
{
if (cvm::get_error() ||
(biases.back()->check_keywords(conf, key) != COLVARS_OK)) {
cvm::log("Error while constructing bias number " +
cvm::to_str(biases.size()) + " : deleting.\n");
delete biases.back(); // the bias destructor updates the biases array
return true;
}
return false;
}
int colvarmodule::parse_biases (std::string const &conf)
{
@ -223,12 +244,7 @@ int colvarmodule::parse_biases (std::string const &conf)
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_abf (abf_conf, "abf"));
if (cvm::get_error()) {
delete biases.back();
biases.pop_back();
return COLVARS_ERROR;
}
if ((biases.back())->check_keywords (abf_conf, "abf") != COLVARS_OK) {
if (cvm::check_new_bias(abf_conf, "abf")) {
return COLVARS_ERROR;
}
cvm::decrease_depth();
@ -250,12 +266,7 @@ int colvarmodule::parse_biases (std::string const &conf)
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_restraint_harmonic (harm_conf, "harmonic"));
if (cvm::get_error()) {
delete biases.back();
biases.pop_back();
return COLVARS_ERROR;
}
if ((biases.back())->check_keywords (harm_conf, "harmonic") != COLVARS_OK) {
if (cvm::check_new_bias(harm_conf, "harmonic")) {
return COLVARS_ERROR;
}
cvm::decrease_depth();
@ -277,12 +288,7 @@ int colvarmodule::parse_biases (std::string const &conf)
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_restraint_linear (lin_conf, "linear"));
if (cvm::get_error()) {
delete biases.back();
biases.pop_back();
return COLVARS_ERROR;
}
if ((biases.back())->check_keywords (lin_conf, "linear") != COLVARS_OK) {
if (cvm::check_new_bias(lin_conf, "linear")) {
return COLVARS_ERROR;
}
cvm::decrease_depth();
@ -304,12 +310,7 @@ int colvarmodule::parse_biases (std::string const &conf)
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_alb (alb_conf, "ALB"));
if (cvm::get_error()) {
delete biases.back();
biases.pop_back();
return COLVARS_ERROR;
}
if ((biases.back())->check_keywords (alb_conf, "ALB") != COLVARS_OK) {
if (cvm::check_new_bias(alb_conf, "ALB")) {
return COLVARS_ERROR;
}
cvm::decrease_depth();
@ -332,12 +333,7 @@ int colvarmodule::parse_biases (std::string const &conf)
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_histogram (histo_conf, "histogram"));
if (cvm::get_error()) {
delete biases.back();
biases.pop_back();
return COLVARS_ERROR;
}
if ((biases.back())->check_keywords (histo_conf, "histogram") != COLVARS_OK) {
if (cvm::check_new_bias(histo_conf, "histogram")) {
return COLVARS_ERROR;
}
cvm::decrease_depth();
@ -359,12 +355,7 @@ int colvarmodule::parse_biases (std::string const &conf)
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_meta (meta_conf, "metadynamics"));
if (cvm::get_error()) {
delete biases.back();
biases.pop_back();
return COLVARS_ERROR;
}
if ((biases.back())->check_keywords (meta_conf, "metadynamics") != COLVARS_OK) {
if (cvm::check_new_bias(meta_conf, "metadynamics")) {
return COLVARS_ERROR;
}
cvm::decrease_depth();
@ -675,21 +666,20 @@ colvarmodule::~colvarmodule()
int colvarmodule::reset()
{
if (cvm::debug())
cvm::log ("colvars::reset() called.\n");
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
cvm::log("Resetting the Collective Variables Module.\n");
// Iterate backwards because we are deleting the elements as we go
for (std::vector<colvar *>::reverse_iterator cvi = colvars.rbegin();
cvi != colvars.rend();
cvi++) {
delete *cvi;
cvi--;
delete *cvi; // the colvar destructor updates the colvars array
}
colvars.clear();
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
// Iterate backwards because we are deleting the elements as we go
for (std::vector<colvarbias *>::reverse_iterator bi = biases.rbegin();
bi != biases.rend();
bi++) {
delete *bi;
bi--;
delete *bi; // the bias destructor updates the biases array
}
biases.clear();

5
lib/colvars/colvarmodule.h
View File

@ -4,7 +4,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2014-10-07"
#define COLVARS_VERSION "2014-10-13"
#endif
#ifndef COLVARS_DEBUG
@ -219,6 +219,9 @@ public:
/// Parse and initialize collective variable biases
int parse_biases (std::string const &conf);
/// Test error condition and keyword parsing
/// on error, delete new bias
bool check_new_bias(std::string &conf, char const *key);
// "Setup" functions (change internal data based on related data
// from the proxy that may change during program execution)

5
lib/colvars/colvarscript.cpp
View File

@ -214,10 +214,7 @@ int colvarscript::proc_colvar (int argc, char const *argv[]) {
}
if (subcmd == "update") {
// note: this is not sufficient for a newly created colvar
// as atom coordinates may not be properly loaded
// a full CVM update is required
// or otherwise updating atom positions
cv->calc();
cv->update();
result = cvm::to_str(cv->value(), 0, cvm::cv_prec);
return COLVARSCRIPT_OK;

40
lib/colvars/colvartypes.cpp
View File

@ -350,22 +350,22 @@ void colvarmodule::rotation::calc_optimal_rotation
// derivative of the S matrix
ds_1.reset();
ds_1[0][0] = cvm::rvector ( a2x, a2y, a2z);
ds_1[1][0] = cvm::rvector ( 0.0, a2z, -a2y);
ds_1[0][0].set( a2x, a2y, a2z);
ds_1[1][0].set( 0.0, a2z, -a2y);
ds_1[0][1] = ds_1[1][0];
ds_1[2][0] = cvm::rvector (-a2z, 0.0, a2x);
ds_1[2][0].set(-a2z, 0.0, a2x);
ds_1[0][2] = ds_1[2][0];
ds_1[3][0] = cvm::rvector ( a2y, -a2x, 0.0);
ds_1[3][0].set( a2y, -a2x, 0.0);
ds_1[0][3] = ds_1[3][0];
ds_1[1][1] = cvm::rvector ( a2x, -a2y, -a2z);
ds_1[2][1] = cvm::rvector ( a2y, a2x, 0.0);
ds_1[1][1].set( a2x, -a2y, -a2z);
ds_1[2][1].set( a2y, a2x, 0.0);
ds_1[1][2] = ds_1[2][1];
ds_1[3][1] = cvm::rvector ( a2z, 0.0, a2x);
ds_1[3][1].set( a2z, 0.0, a2x);
ds_1[1][3] = ds_1[3][1];
ds_1[2][2] = cvm::rvector (-a2x, a2y, -a2z);
ds_1[3][2] = cvm::rvector ( 0.0, a2z, a2y);
ds_1[2][2].set(-a2x, a2y, -a2z);
ds_1[3][2].set( 0.0, a2z, a2y);
ds_1[2][3] = ds_1[3][2];
ds_1[3][3] = cvm::rvector (-a2x, -a2y, a2z);
ds_1[3][3].set(-a2x, -a2y, a2z);
cvm::rvector &dl0_1 = dL0_1[ia];
vector1d<cvm::rvector, 4> &dq0_1 = dQ0_1[ia];
@ -404,22 +404,22 @@ void colvarmodule::rotation::calc_optimal_rotation
matrix2d<cvm::rvector, 4, 4> &ds_2 = dS_2[ia];
ds_2.reset();
ds_2[0][0] = cvm::rvector ( a1x, a1y, a1z);
ds_2[1][0] = cvm::rvector ( 0.0, -a1z, a1y);
ds_2[0][0].set( a1x, a1y, a1z);
ds_2[1][0].set( 0.0, -a1z, a1y);
ds_2[0][1] = ds_2[1][0];
ds_2[2][0] = cvm::rvector ( a1z, 0.0, -a1x);
ds_2[2][0].set( a1z, 0.0, -a1x);
ds_2[0][2] = ds_2[2][0];
ds_2[3][0] = cvm::rvector (-a1y, a1x, 0.0);
ds_2[3][0].set(-a1y, a1x, 0.0);
ds_2[0][3] = ds_2[3][0];
ds_2[1][1] = cvm::rvector ( a1x, -a1y, -a1z);
ds_2[2][1] = cvm::rvector ( a1y, a1x, 0.0);
ds_2[1][1].set( a1x, -a1y, -a1z);
ds_2[2][1].set( a1y, a1x, 0.0);
ds_2[1][2] = ds_2[2][1];
ds_2[3][1] = cvm::rvector ( a1z, 0.0, a1x);
ds_2[3][1].set( a1z, 0.0, a1x);
ds_2[1][3] = ds_2[3][1];
ds_2[2][2] = cvm::rvector (-a1x, a1y, -a1z);
ds_2[3][2] = cvm::rvector ( 0.0, a1z, a1y);
ds_2[2][2].set(-a1x, a1y, -a1z);
ds_2[3][2].set( 0.0, a1z, a1y);
ds_2[2][3] = ds_2[3][2];
ds_2[3][3] = cvm::rvector (-a1x, -a1y, a1z);
ds_2[3][3].set(-a1x, -a1y, a1z);
cvm::rvector &dl0_2 = dL0_2[ia];
vector1d<cvm::rvector, 4> &dq0_2 = dQ0_2[ia];

11
lib/colvars/colvartypes.h
View File

@ -37,10 +37,19 @@ public:
{}
/// \brief Set all components to a scalar value
inline void set (cvm::real const &value = 0.0) {
inline void set (cvm::real const &value) {
x = y = z = value;
}
/// \brief Assign all components
inline void set (cvm::real const &x_i,
cvm::real const &y_i,
cvm::real const &z_i) {
x = x_i;
y = y_i;
z = z_i;
}
/// \brief Set all components to zero
inline void reset() {
x = y = z = 0.0;

10
src/USER-COLVARS/colvarproxy_lammps.cpp
View File

@ -90,7 +90,7 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
// output prefix is always given
output_prefix_str = std::string(out_name);
// not so for restarts
restart_prefix_str = std::string("rest");
restart_output_prefix_str = std::string("rest");
// check if it is possible to save output configuration
if ((!output_prefix_str.size()) && (!restart_output_prefix_str.size())) {
@ -101,13 +101,13 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
// 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)) {
restart_prefix_str = std::string(outp->restart1);
restart_output_prefix_str = std::string(outp->restart1);
} else if ((outp->restart_every_double > 0) && (outp->restart2a != 0)) {
restart_prefix_str = std::string(outp->restart2a);
restart_output_prefix_str = std::string(outp->restart2a);
}
// trim off unwanted stuff from the restart prefix
if (restart_prefix_str.rfind(".*") != std::string::npos)
restart_prefix_str.erase(restart_prefix_str.rfind(".*"),2);
if (restart_output_prefix_str.rfind(".*") != std::string::npos)
restart_output_prefix_str.erase(restart_output_prefix_str.rfind(".*"),2);
}

7
src/USER-COLVARS/colvarproxy_lammps.h
View File

@ -44,10 +44,6 @@ class colvarproxy_lammps : public colvarproxy {
int restart_every;
int previous_step;
std::string input_prefix_str;
std::string output_prefix_str;
std::string restart_prefix_str;
bool first_timestep;
bool system_force_requested;
bool do_exit;
@ -102,9 +98,6 @@ class colvarproxy_lammps : public colvarproxy {
cvm::real temperature() { return t_target; };
cvm::real dt() { return _lmp->update->dt * _lmp->force->femtosecond; };
inline std::string input_prefix() { return input_prefix_str; };
inline std::string output_prefix() { return output_prefix_str; };
inline std::string restart_output_prefix() { return restart_prefix_str; };
inline size_t restart_frequency() { return restart_every; };
void add_energy (cvm::real energy) { bias_energy = energy; };