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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10118 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-06-27 22:48:27 +00:00
parent 38112d0063
commit 4da20dce99
30 changed files with 883 additions and 571 deletions
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57
lib/colvars/colvaratoms.cpp
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@ -26,8 +26,8 @@ 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_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), b_fit_gradients (false),
noforce (false)
{
this->reserve (atoms.size());
@ -43,8 +43,8 @@ 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_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), b_fit_gradients (false),
noforce (false)
{
total_mass = 0.0;
@ -71,6 +71,18 @@ void cvm::atom_group::add_atom (cvm::atom const &a)
}
void cvm::atom_group::reset_mass(std::string &name, int i, int j)
{
total_mass = 0.0;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
total_mass += ai->mass;
}
cvm::log ("Re-initialized atom group "+name+":"+cvm::to_str (i)+"/"+
cvm::to_str (j)+". "+ cvm::to_str (this->size())+
" atoms: total mass = "+cvm::to_str (this->total_mass)+".\n");
}
void cvm::atom_group::parse (std::string const &conf,
char const *key)
{
@ -129,6 +141,25 @@ void cvm::atom_group::parse (std::string const &conf,
atom_indexes.clear();
}
std::string index_group_name;
if (get_keyval (group_conf, "indexGroup", index_group_name)) {
// use an index group from the index file read globally
std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
std::list<std::vector<int> >::iterator index_groups_i = cvm::index_groups.begin();
for ( ; names_i != cvm::index_group_names.end() ; names_i++, index_groups_i++) {
if (*names_i == index_group_name)
break;
}
if (names_i == cvm::index_group_names.end()) {
cvm::fatal_error ("Error: could not find index group "+
index_group_name+" among those provided by the index file.\n");
}
this->reserve (index_groups_i->size());
for (size_t i = 0; i < index_groups_i->size(); i++) {
this->push_back (cvm::atom ((*index_groups_i)[i]));
}
}
}
{
@ -234,7 +265,7 @@ void cvm::atom_group::parse (std::string const &conf,
}
}
for (std::vector<cvm::atom>::iterator a1 = this->begin();
for (std::vector<cvm::atom>::iterator a1 = this->begin();
a1 != this->end(); a1++) {
std::vector<cvm::atom>::iterator a2 = a1;
++a2;
@ -253,10 +284,10 @@ void cvm::atom_group::parse (std::string const &conf,
if (get_keyval (group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos(), mode)) {
b_dummy = true;
this->total_mass = 1.0;
} else
} else
b_dummy = false;
if (b_dummy && (this->size()))
if (b_dummy && (this->size()))
cvm::fatal_error ("Error: cannot set up group \""+
std::string (key)+"\" as a dummy atom "
"and provide it with atom definitions.\n");
@ -328,7 +359,7 @@ void cvm::atom_group::parse (std::string const &conf,
std::string ref_pos_col;
double ref_pos_col_value;
if (get_keyval (group_conf, "refPositionsCol", ref_pos_col, std::string (""), mode)) {
// if provided, use PDB column to select coordinates
bool found = get_keyval (group_conf, "refPositionsColValue", ref_pos_col_value, 0.0, mode);
@ -486,7 +517,7 @@ void cvm::atom_group::calc_apply_roto_translation()
}
}
void cvm::atom_group::apply_translation (cvm::rvector const &t)
void cvm::atom_group::apply_translation (cvm::rvector const &t)
{
if (b_dummy) return;
@ -496,7 +527,7 @@ void cvm::atom_group::apply_translation (cvm::rvector const &t)
}
}
void cvm::atom_group::apply_rotation (cvm::rotation const &rot)
void cvm::atom_group::apply_rotation (cvm::rotation const &rot)
{
if (b_dummy) return;
@ -617,11 +648,11 @@ void cvm::atom_group::calc_fit_gradients()
}
if (b_rotate) {
// add the rotation matrix contribution to the gradients
cvm::rotation const rot_inv = rot.inverse();
cvm::atom_pos const cog = this->center_of_geometry();
for (size_t i = 0; i < this->size(); i++) {
cvm::atom_pos const pos_orig = rot_inv.rotate ((b_center ? ((*this)[i].pos - cog) : ((*this)[i].pos)));
@ -785,7 +816,7 @@ void cvm::atom_group::apply_force (cvm::rvector const &force)
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force ((ai->mass/this->total_mass) * force);
}
}
}
}