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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11969 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-05-12 15:08:14 +00:00
parent fd1b9f2c5c
commit d17c0325d4
9 changed files with 61 additions and 55 deletions
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7
lib/colvars/colvar.cpp
View File

@ -591,11 +591,12 @@ void colvar::enable (colvar::task const &t)
}
break;
case task_output_value:
case task_runave:
case task_corrfunc:
case task_ntot:
case task_langevin:
case task_output_energy:
break;
case task_gradients:
@ -612,6 +613,7 @@ void colvar::enable (colvar::task const &t)
build_atom_list();
}
break;
}
@ -660,6 +662,9 @@ void colvar::disable (colvar::task const &t)
case task_lower_wall:
case task_upper_wall:
case task_ntot:
case task_langevin:
case task_output_energy:
case task_collect_gradients:
break;
}

6
lib/colvars/colvaratoms.cpp
View File

@ -14,8 +14,8 @@
cvm::atom_group::atom_group (std::string const &conf,
char const *key)
: b_center (false), b_rotate (false), b_user_defined_fit (false),
ref_pos_group (NULL),
b_fit_gradients (false),
ref_pos_group (NULL),
noforce (false)
{
cvm::log ("Defining atom group \""+
@ -27,7 +27,7 @@ cvm::atom_group::atom_group (std::string const &conf,
cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
: b_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), b_fit_gradients (false),
b_fit_gradients (false), ref_pos_group (NULL),
noforce (false)
{
this->reserve (atoms.size());
@ -44,7 +44,7 @@ cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
cvm::atom_group::atom_group()
: b_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), b_fit_gradients (false),
b_fit_gradients (false), ref_pos_group (NULL),
noforce (false)
{
total_mass = 0.0;

4
lib/colvars/colvarbias.cpp
View File

@ -121,8 +121,8 @@ std::ostream & colvarbias::write_traj (std::ostream &os)
colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
char const *key)
: colvarbias (conf, key),
target_nsteps (0),
target_nstages (0)
target_nstages (0),
target_nsteps (0)
{
get_keyval (conf, "forceConstant", force_k, 1.0);
for (size_t i = 0; i < colvars.size(); i++) {

8
lib/colvars/colvarbias_meta.cpp
View File

@ -25,16 +25,16 @@
colvarbias_meta::colvarbias_meta()
: colvarbias(),
state_file_step (0),
new_hills_begin (hills.end())
new_hills_begin (hills.end()),
state_file_step (0)
{
}
colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
: colvarbias (conf, key),
state_file_step (0),
new_hills_begin (hills.end())
new_hills_begin (hills.end()),
state_file_step (0)
{
if (cvm::n_abf_biases > 0)
cvm::log ("Warning: running ABF and metadynamics together is not recommended unless applyBias is off for ABF.\n");

8
lib/colvars/colvarcomp.cpp
View File

@ -8,18 +8,18 @@
colvar::cvc::cvc()
: sup_coeff (1.0), sup_np (1),
b_periodic (false),
b_debug_gradients (false),
b_inverse_gradients (false),
b_Jacobian_derivative (false)
b_Jacobian_derivative (false),
b_debug_gradients (false)
{}
colvar::cvc::cvc (std::string const &conf)
: sup_coeff (1.0), sup_np (1),
b_periodic (false),
b_debug_gradients (false),
b_inverse_gradients (false),
b_Jacobian_derivative (false)
b_Jacobian_derivative (false),
b_debug_gradients (false)
{
if (cvm::debug())
cvm::log ("Initializing cvc base object.\n");

10
lib/colvars/colvargrid.h
View File

@ -173,19 +173,19 @@ public:
/// \brief "Almost copy-constructor": only copies configuration
/// parameters from another grid, but doesn't reallocate stuff;
/// create() must be called after that;
colvar_grid (colvar_grid<T> const &g) : has_data (false),
nd (g.nd),
colvar_grid (colvar_grid<T> const &g) : nd (g.nd),
nx (g.nx),
mult (g.mult),
data(),
cv (g.cv),
actual_value (g.actual_value),
lower_boundaries (g.lower_boundaries),
upper_boundaries (g.upper_boundaries),
periodic (g.periodic),
hard_lower_boundaries (g.hard_lower_boundaries),
hard_upper_boundaries (g.hard_upper_boundaries),
periodic (g.periodic),
widths (g.widths),
actual_value (g.actual_value),
data()
has_data (false)
{
save_delimiters = false;
}

35
lib/colvars/colvarmodule.cpp
View File

@ -815,6 +815,41 @@ void cvm::read_index_file (char const *filename)
}
void cvm::load_atoms (char const *file_name,
std::vector<cvm::atom> &atoms,
std::string const &pdb_field,
double const pdb_field_value)
{
proxy->load_atoms (file_name, atoms, pdb_field, pdb_field_value);
}
void cvm::load_coords (char const *file_name,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field,
double const pdb_field_value)
{
// Differentiate between PDB and XYZ files
// for XYZ files, use CVM internal parser
// otherwise call proxy function for PDB
std::string const ext (strlen(file_name) > 4 ? (file_name + (strlen(file_name) - 4)) : file_name);
if (colvarparse::to_lower_cppstr (ext) == std::string (".xyz")) {
if ( pdb_field.size() > 0 ) {
cvm::fatal_error ("Error: PDB column may not be specified for XYZ coordinate file.\n");
}
cvm::load_coords_xyz (file_name, pos, indices);
} else {
proxy->load_coords (file_name, pos, indices, pdb_field, pdb_field_value);
}
}
void cvm::backup_file (char const *filename)
{
proxy->backup_file (filename);
}
void cvm::load_coords_xyz (char const *filename,
std::vector<atom_pos> &pos,
const std::vector<int> &indices)

36
lib/colvars/colvarmodule.h
View File

@ -2,7 +2,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2013-12-13"
#define COLVARS_VERSION "2014-05-08"
#endif
#ifndef COLVARS_DEBUG
@ -483,40 +483,6 @@ inline cvm::real cvm::position_dist2 (cvm::atom_pos const &pos1,
return proxy->position_dist2 (pos1, pos2);
}
inline void cvm::load_atoms (char const *file_name,
std::vector<cvm::atom> &atoms,
std::string const &pdb_field,
double const pdb_field_value)
{
proxy->load_atoms (file_name, atoms, pdb_field, pdb_field_value);
}
inline void cvm::load_coords (char const *file_name,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field,
double const pdb_field_value)
{
// Differentiate between PDB and XYZ files
// for XYZ files, use CVM internal parser
// otherwise call proxy function for PDB
char const *ext = strlen(file_name) > 4 ? file_name + (strlen(file_name) - 4) : file_name;
if ( !strncmp(ext, ".xyz", 4) || !strncmp(ext, ".XYZ", 4) ) {
if ( pdb_field.size() > 0 ) {
cvm::fatal_error ("Error: PDB column may not be specified for XYZ coordinate file.\n");
}
cvm::load_coords_xyz (file_name, pos, indices);
} else {
proxy->load_coords (file_name, pos, indices, pdb_field, pdb_field_value);
}
}
inline void cvm::backup_file (char const *filename)
{
proxy->backup_file (filename);
}
inline cvm::real cvm::rand_gaussian (void)
{
return proxy->rand_gaussian();

2
lib/colvars/colvarparse.cpp
View File

@ -595,7 +595,7 @@ std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
size_t brace_count = 1;
std::string line;
while (colvarparse::getline_nocomments (is, line)) {
size_t br = 0, br_old;
size_t br = 0, br_old = 0;
while ( (br = line.find_first_of ("{}", br)) != std::string::npos) {
if (line[br] == '{') brace_count++;
if (line[br] == '}') brace_count--;