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

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12811 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-12-02 02:09:53 +00:00
parent 9c0f849594
commit c4af1cdbbd
34 changed files with 5927 additions and 4786 deletions
Download Patch File Download Diff File Expand all files Collapse all files

140
lib/colvars/colvarcomp_coordnums.cpp
View File

@ -12,21 +12,21 @@
template<bool calculate_gradients>
cvm::real colvar::coordnum::switching_function (cvm::real const &r0,
cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance (A1.pos, A2.pos);
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::real const l2 = diff.norm2()/(r0*r0);
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow (l2, en2);
cvm::real const xd = std::pow (l2, ed2);
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
@ -41,27 +41,27 @@ cvm::real colvar::coordnum::switching_function (cvm::real const &r0,
template<bool calculate_gradients>
cvm::real colvar::coordnum::switching_function (cvm::rvector const &r0_vec,
cvm::real colvar::coordnum::switching_function(cvm::rvector const &r0_vec,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance (A1.pos, A2.pos);
cvm::rvector const scal_diff (diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::rvector const scal_diff(diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
cvm::real const l2 = scal_diff.norm2();
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow (l2, en2);
cvm::real const xd = std::pow (l2, ed2);
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
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,
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);
A1.grad += (-1.0)*dFdl2*dl2dx;
@ -72,29 +72,29 @@ cvm::real colvar::coordnum::switching_function (cvm::rvector const &r0_vec,
colvar::coordnum::coordnum (std::string const &conf)
: distance (conf), b_anisotropic (false), b_group2_center_only (false)
colvar::coordnum::coordnum(std::string const &conf)
: distance(conf), b_anisotropic(false), b_group2_center_only(false)
{
function_type = "coordnum";
x.type (colvarvalue::type_scalar);
x.type(colvarvalue::type_scalar);
// group1 and group2 are already initialized by distance()
if (group1.b_dummy)
cvm::fatal_error ("Error: only group2 is allowed to be a dummy atom\n");
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;
bool const b_scale = get_keyval (conf, "cutoff", r0,
cvm::real (4.0 * cvm::unit_angstrom()));
bool const b_scale = get_keyval(conf, "cutoff", r0,
cvm::real(4.0 * cvm::unit_angstrom()));
if (get_keyval (conf, "cutoff3", r0_vec,
cvm::rvector (4.0, 4.0, 4.0), parse_silent)) {
if (get_keyval(conf, "cutoff3", r0_vec,
cvm::rvector(4.0, 4.0, 4.0), parse_silent)) {
if (b_scale)
cvm::fatal_error ("Error: cannot specify \"scale\" and "
cvm::fatal_error("Error: cannot specify \"scale\" and "
"\"scale3\" at the same time.\n");
b_anisotropic = true;
// remove meaningless negative signs
@ -103,22 +103,22 @@ colvar::coordnum::coordnum (std::string const &conf)
if (r0_vec.z < 0.0) r0_vec.z *= -1.0;
}
get_keyval (conf, "expNumer", en, int (6) );
get_keyval (conf, "expDenom", ed, int (12));
get_keyval(conf, "expNumer", en, int(6) );
get_keyval(conf, "expDenom", ed, int(12));
if ( (en%2) || (ed%2) ) {
cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n");
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);
}
colvar::coordnum::coordnum()
: b_anisotropic (false), b_group2_center_only (false)
: b_anisotropic(false), b_group2_center_only(false)
{
function_type = "coordnum";
x.type (colvarvalue::type_scalar);
x.type(colvarvalue::type_scalar);
}
@ -174,7 +174,7 @@ void colvar::coordnum::calc_gradients()
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 {
@ -193,86 +193,86 @@ void colvar::coordnum::calc_gradients()
// if (cvm::debug()) {
// for (size_t i = 0; i < group1.size(); i++) {
// cvm::log ("atom["+cvm::to_str (group1[i].id+1)+"] gradient: "+
// 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::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)
void colvar::coordnum::apply_force(colvarvalue const &force)
{
if (!group1.noforce)
group1.apply_colvar_force (force.real_value);
group1.apply_colvar_force(force.real_value);
if (!group2.noforce)
group2.apply_colvar_force (force.real_value);
group2.apply_colvar_force(force.real_value);
}
// h_bond member functions
colvar::h_bond::h_bond (std::string const &conf)
: cvc (conf)
colvar::h_bond::h_bond(std::string const &conf)
: cvc(conf)
{
if (cvm::debug())
cvm::log ("Initializing h_bond object.\n");
cvm::log("Initializing h_bond object.\n");
function_type = "h_bond";
x.type (colvarvalue::type_scalar);
x.type(colvarvalue::type_scalar);
int a_num, d_num;
get_keyval (conf, "acceptor", a_num, -1);
get_keyval (conf, "donor", d_num, -1);
get_keyval(conf, "acceptor", a_num, -1);
get_keyval(conf, "donor", d_num, -1);
if ( (a_num == -1) || (d_num == -1) ) {
cvm::fatal_error ("Error: either acceptor or donor undefined.\n");
cvm::fatal_error("Error: either acceptor or donor undefined.\n");
}
acceptor = cvm::atom (a_num);
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);
acceptor = cvm::atom(a_num);
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);
get_keyval (conf, "cutoff", r0, (3.3 * cvm::unit_angstrom()));
get_keyval (conf, "expNumer", en, 6);
get_keyval (conf, "expDenom", ed, 8);
get_keyval(conf, "cutoff", r0, (3.3 * cvm::unit_angstrom()));
get_keyval(conf, "expNumer", en, 6);
get_keyval(conf, "expDenom", ed, 8);
if ( (en%2) || (ed%2) ) {
cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n");
cvm::fatal_error("Error: odd exponents provided, can only use even ones.\n");
}
if (cvm::debug())
cvm::log ("Done initializing h_bond object.\n");
cvm::log("Done initializing h_bond object.\n");
}
colvar::h_bond::h_bond (cvm::atom const &acceptor_i,
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)
: acceptor(acceptor_i),
donor(donor_i),
r0(r0_i), en(en_i), ed(ed_i)
{
function_type = "h_bond";
x.type (colvarvalue::type_scalar);
x.type(colvarvalue::type_scalar);
atom_groups.push_back (new cvm::atom_group);
atom_groups[0]->add_atom (acceptor);
atom_groups[0]->add_atom (donor);
atom_groups.push_back(new cvm::atom_group);
atom_groups[0]->add_atom(acceptor);
atom_groups[0]->add_atom(donor);
}
colvar::h_bond::h_bond()
: cvc ()
: cvc()
{
function_type = "h_bond";
x.type (colvarvalue::type_scalar);
x.type(colvarvalue::type_scalar);
}
@ -298,20 +298,20 @@ void colvar::h_bond::calc_gradients()
}
void colvar::h_bond::apply_force (colvarvalue const &force)
void colvar::h_bond::apply_force(colvarvalue const &force)
{
acceptor.apply_force (force.real_value * acceptor.grad);
acceptor.apply_force(force.real_value * acceptor.grad);
donor.apply_force (force.real_value * donor.grad);
}
colvar::selfcoordnum::selfcoordnum (std::string const &conf)
: distance (conf, false)
colvar::selfcoordnum::selfcoordnum(std::string const &conf)
: distance(conf, false)
{
function_type = "selfcoordnum";
x.type (colvarvalue::type_scalar);
x.type(colvarvalue::type_scalar);
// group1 is already initialized by distance()
@ -319,12 +319,12 @@ colvar::selfcoordnum::selfcoordnum (std::string const &conf)
// has set it to true
b_inverse_gradients = false;
get_keyval (conf, "cutoff", r0, cvm::real (4.0 * cvm::unit_angstrom()));
get_keyval (conf, "expNumer", en, int (6) );
get_keyval (conf, "expDenom", ed, int (12));
get_keyval(conf, "cutoff", r0, cvm::real(4.0 * cvm::unit_angstrom()));
get_keyval(conf, "expNumer", en, int(6) );
get_keyval(conf, "expDenom", ed, int(12));
if ( (en%2) || (ed%2) ) {
cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n");
cvm::fatal_error("Error: odd exponents provided, can only use even ones.\n");
}
}
@ -332,7 +332,7 @@ colvar::selfcoordnum::selfcoordnum (std::string const &conf)
colvar::selfcoordnum::selfcoordnum()
{
function_type = "selfcoordnum";
x.type (colvarvalue::type_scalar);
x.type(colvarvalue::type_scalar);
}
@ -353,9 +353,9 @@ void colvar::selfcoordnum::calc_gradients()
colvar::coordnum::switching_function<true> (r0, en, ed, group1[i], group1[j]);
}
void colvar::selfcoordnum::apply_force (colvarvalue const &force)
void colvar::selfcoordnum::apply_force(colvarvalue const &force)
{
if (!group1.noforce)
group1.apply_colvar_force (force.real_value);
group1.apply_colvar_force(force.real_value);
}