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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13126 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-02-19 18:20:52 +00:00
parent f300f2367e
commit 067833cf07
21 changed files with 597 additions and 360 deletions
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79
lib/colvars/colvarcomp_coordnums.cpp
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@ -62,8 +62,8 @@ cvm::real colvar::coordnum::switching_function(cvm::rvector const &r0_vec,
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx((2.0/(r0_vec.x*r0_vec.x))*diff.x,
(2.0/(r0_vec.y*r0_vec.y))*diff.y,
(2.0/(r0_vec.z*r0_vec.z))*diff.z);
(2.0/(r0_vec.y*r0_vec.y))*diff.y,
(2.0/(r0_vec.z*r0_vec.z))*diff.z);
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
@ -134,10 +134,10 @@ void colvar::coordnum::calc_value()
if (b_anisotropic) {
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);
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++)
x.real_value += switching_function<false> (r0, en, ed, *ai1, group2_com_atom);
x.real_value += switching_function<false>(r0, en, ed, *ai1, group2_com_atom);
}
} else {
@ -145,12 +145,12 @@ void colvar::coordnum::calc_value()
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++) {
x.real_value += switching_function<false> (r0_vec, en, ed, *ai1, *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++) {
x.real_value += switching_function<false> (r0, en, ed, *ai1, *ai2);
x.real_value += switching_function<false>(r0, en, ed, *ai1, *ai2);
}
}
}
@ -168,10 +168,10 @@ void colvar::coordnum::calc_gradients()
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
switching_function<true> (r0_vec, en, ed, *ai1, group2_com_atom);
switching_function<true>(r0_vec, en, ed, *ai1, group2_com_atom);
} else {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
switching_function<true> (r0, en, ed, *ai1, group2_com_atom);
switching_function<true>(r0, en, ed, *ai1, group2_com_atom);
}
group2.set_weighted_gradient(group2_com_atom.grad);
@ -181,27 +181,15 @@ void colvar::coordnum::calc_gradients()
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++) {
switching_function<true> (r0_vec, en, ed, *ai1, *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++) {
switching_function<true> (r0, en, ed, *ai1, *ai2);
switching_function<true>(r0, en, ed, *ai1, *ai2);
}
}
}
// if (cvm::debug()) {
// for (size_t i = 0; i < group1.size(); i++) {
// cvm::log("atom["+cvm::to_str (group1[i].id+1)+"] gradient: "+
// cvm::to_str (group1[i].grad)+"\n");
// }
// for (size_t i = 0; i < group2.size(); i++) {
// cvm::log("atom["+cvm::to_str (group2[i].id+1)+"] gradient: "+
// cvm::to_str (group2[i].grad)+"\n");
// }
// }
}
void colvar::coordnum::apply_force(colvarvalue const &force)
@ -234,8 +222,8 @@ colvar::h_bond::h_bond(std::string const &conf)
cvm::fatal_error("Error: either acceptor or donor undefined.\n");
}
acceptor = cvm::atom(a_num);
donor = cvm::atom(d_num);
cvm::atom acceptor = cvm::atom(a_num);
cvm::atom donor = cvm::atom(d_num);
atom_groups.push_back(new cvm::atom_group);
atom_groups[0]->add_atom(acceptor);
atom_groups[0]->add_atom(donor);
@ -253,12 +241,10 @@ colvar::h_bond::h_bond(std::string const &conf)
}
colvar::h_bond::h_bond(cvm::atom const &acceptor_i,
cvm::atom const &donor_i,
cvm::real r0_i, int en_i, int ed_i)
: acceptor(acceptor_i),
donor(donor_i),
r0(r0_i), en(en_i), ed(ed_i)
colvar::h_bond::h_bond(cvm::atom const &acceptor,
cvm::atom const &donor,
cvm::real r0_i, int en_i, int ed_i)
: r0(r0_i), en(en_i), ed(ed_i)
{
function_type = "h_bond";
x.type(colvarvalue::type_scalar);
@ -278,30 +264,25 @@ colvar::h_bond::h_bond()
colvar::h_bond::~h_bond()
{
for (unsigned int i=0; i<atom_groups.size(); i++) {
delete atom_groups[i];
}
delete atom_groups[0];
}
void colvar::h_bond::calc_value()
{
x.real_value = colvar::coordnum::switching_function<false> (r0, en, ed, acceptor, donor);
x.real_value = colvar::coordnum::switching_function<false>(r0, en, ed, (*atom_groups[0])[0], (*atom_groups[0])[1]);
}
void colvar::h_bond::calc_gradients()
{
colvar::coordnum::switching_function<true> (r0, en, ed, acceptor, donor);
(*atom_groups[0])[0].grad = acceptor.grad;
(*atom_groups[0])[1].grad = donor.grad;
colvar::coordnum::switching_function<true>(r0, en, ed, (*atom_groups[0])[0], (*atom_groups[0])[1]);
}
void colvar::h_bond::apply_force(colvarvalue const &force)
{
acceptor.apply_force(force.real_value * acceptor.grad);
donor.apply_force (force.real_value * donor.grad);
(atom_groups[0])->apply_colvar_force(force);
}
@ -339,23 +320,27 @@ 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]);
}
}
}
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)
if (!group1.noforce) {
group1.apply_colvar_force(force.real_value);
}
}