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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14829 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-04-15 16:07:01 +00:00
parent 32509da721
commit 212a955285
31 changed files with 1713 additions and 1493 deletions
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63
lib/colvars/colvarcomp_coordnums.cpp
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@ -79,13 +79,13 @@ colvar::coordnum::coordnum(std::string const &conf)
x.type(colvarvalue::type_scalar);
// group1 and group2 are already initialized by distance()
if (group1.b_dummy)
if (group1->b_dummy)
cvm::fatal_error("Error: only group2 is allowed to be a dummy atom\n");
// need to specify this explicitly because the distance() constructor
// has set it to true
b_inverse_gradients = false;
feature_states[f_cvc_inv_gradient]->available = false;
bool const b_scale = get_keyval(conf, "cutoff", r0,
cvm::real(4.0 * cvm::unit_angstrom()));
@ -110,7 +110,7 @@ colvar::coordnum::coordnum(std::string const &conf)
cvm::fatal_error("Error: odd exponents provided, can only use even ones.\n");
}
get_keyval(conf, "group2CenterOnly", b_group2_center_only, group2.b_dummy);
get_keyval(conf, "group2CenterOnly", b_group2_center_only, group2->b_dummy);
}
@ -130,26 +130,26 @@ void colvar::coordnum::calc_value()
// create a fake atom to hold the group2 com coordinates
cvm::atom group2_com_atom;
group2_com_atom.pos = group2.center_of_mass();
group2_com_atom.pos = group2->center_of_mass();
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
x.real_value += switching_function<false>(r0_vec, en, ed, *ai1, group2_com_atom);
} else {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
x.real_value += switching_function<false>(r0, en, ed, *ai1, group2_com_atom);
}
} else {
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
x.real_value += switching_function<false>(r0_vec, en, ed, *ai1, *ai2);
}
} else {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
x.real_value += switching_function<false>(r0, en, ed, *ai1, *ai2);
}
}
@ -163,29 +163,29 @@ void colvar::coordnum::calc_gradients()
// create a fake atom to hold the group2 com coordinates
cvm::atom group2_com_atom;
group2_com_atom.pos = group2.center_of_mass();
group2_com_atom.pos = group2->center_of_mass();
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
switching_function<true>(r0_vec, en, ed, *ai1, group2_com_atom);
} else {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
switching_function<true>(r0, en, ed, *ai1, group2_com_atom);
}
group2.set_weighted_gradient(group2_com_atom.grad);
group2->set_weighted_gradient(group2_com_atom.grad);
} else {
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
switching_function<true>(r0_vec, en, ed, *ai1, *ai2);
}
} else {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
switching_function<true>(r0, en, ed, *ai1, *ai2);
}
}
@ -194,11 +194,11 @@ void colvar::coordnum::calc_gradients()
void colvar::coordnum::apply_force(colvarvalue const &force)
{
if (!group1.noforce)
group1.apply_colvar_force(force.real_value);
if (!group1->noforce)
group1->apply_colvar_force(force.real_value);
if (!group2.noforce)
group2.apply_colvar_force(force.real_value);
if (!group2->noforce)
group2->apply_colvar_force(force.real_value);
}
@ -298,7 +298,8 @@ colvar::selfcoordnum::selfcoordnum(std::string const &conf)
// need to specify this explicitly because the distance() constructor
// has set it to true
b_inverse_gradients = false;
feature_states[f_cvc_inv_gradient]->available = false;
get_keyval(conf, "cutoff", r0, cvm::real(4.0 * cvm::unit_angstrom()));
get_keyval(conf, "expNumer", en, int(6) );
@ -320,9 +321,9 @@ colvar::selfcoordnum::selfcoordnum()
void colvar::selfcoordnum::calc_value()
{
x.real_value = 0.0;
for (size_t i = 0; i < group1.size() - 1; i++) {
for (size_t j = i + 1; j < group1.size(); j++) {
x.real_value += colvar::coordnum::switching_function<false>(r0, en, ed, group1[i], group1[j]);
for (size_t i = 0; i < group1->size() - 1; i++) {
for (size_t j = i + 1; j < group1->size(); j++) {
x.real_value += colvar::coordnum::switching_function<false>(r0, en, ed, (*group1)[i], (*group1)[j]);
}
}
}
@ -330,17 +331,17 @@ void colvar::selfcoordnum::calc_value()
void colvar::selfcoordnum::calc_gradients()
{
for (size_t i = 0; i < group1.size() - 1; i++) {
for (size_t j = i + 1; j < group1.size(); j++) {
colvar::coordnum::switching_function<true>(r0, en, ed, group1[i], group1[j]);
for (size_t i = 0; i < group1->size() - 1; i++) {
for (size_t j = i + 1; j < group1->size(); j++) {
colvar::coordnum::switching_function<true>(r0, en, ed, (*group1)[i], (*group1)[j]);
}
}
}
void colvar::selfcoordnum::apply_force(colvarvalue const &force)
{
if (!group1.noforce) {
group1.apply_colvar_force(force.real_value);
if (!group1->noforce) {
group1->apply_colvar_force(force.real_value);
}
}