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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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249
lib/colvars/colvarcomp_angles.cpp
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@ -11,14 +11,13 @@ colvar::angle::angle(std::string const &conf)
: cvc(conf)
{
function_type = "angle";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
parse_group(conf, "group1", group1);
parse_group(conf, "group2", group2);
parse_group(conf, "group3", group3);
atom_groups.push_back(&group1);
atom_groups.push_back(&group2);
atom_groups.push_back(&group3);
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3");
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing system force on group 1 only");
}
@ -27,19 +26,21 @@ colvar::angle::angle(std::string const &conf)
colvar::angle::angle(cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3)
: group1(std::vector<cvm::atom>(1, a1)),
group2(std::vector<cvm::atom>(1, a2)),
group3(std::vector<cvm::atom>(1, a3))
cvm::atom const &a2,
cvm::atom const &a3)
{
function_type = "angle";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
b_1site_force = false;
atom_groups.push_back(&group1);
atom_groups.push_back(&group2);
atom_groups.push_back(&group3);
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
group3 = new cvm::atom_group(std::vector<cvm::atom>(1, a3));
atom_groups.push_back(group1);
atom_groups.push_back(group2);
atom_groups.push_back(group3);
x.type(colvarvalue::type_scalar);
}
@ -54,9 +55,9 @@ colvar::angle::angle()
void colvar::angle::calc_value()
{
cvm::atom_pos const g1_pos = group1.center_of_mass();
cvm::atom_pos const g2_pos = group2.center_of_mass();
cvm::atom_pos const g3_pos = group3.center_of_mass();
cvm::atom_pos const g1_pos = group1->center_of_mass();
cvm::atom_pos const g2_pos = group2->center_of_mass();
cvm::atom_pos const g3_pos = group3->center_of_mass();
r21 = cvm::position_distance(g2_pos, g1_pos);
r21l = r21.norm();
@ -71,7 +72,6 @@ void colvar::angle::calc_value()
void colvar::angle::calc_gradients()
{
size_t i;
cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
cvm::real const dxdcos = -1.0 / std::sqrt(1.0 - cos_theta*cos_theta);
@ -81,22 +81,11 @@ void colvar::angle::calc_gradients()
dxdr3 = (180.0/PI) * dxdcos *
(1.0/r23l) * ( r21/r21l + (-1.0) * cos_theta * r23/r23l );
for (i = 0; i < group1.size(); i++) {
group1[i].grad = (group1[i].mass/group1.total_mass) *
(dxdr1);
}
group1->set_weighted_gradient(dxdr1);
group2->set_weighted_gradient((dxdr1 + dxdr3) * (-1.0));
group3->set_weighted_gradient(dxdr3);
for (i = 0; i < group2.size(); i++) {
group2[i].grad = (group2[i].mass/group2.total_mass) *
(dxdr1 + dxdr3) * (-1.0);
}
for (i = 0; i < group3.size(); i++) {
group3[i].grad = (group3[i].mass/group3.total_mass) *
(dxdr3);
}
if (b_debug_gradients) {
if (is_enabled(f_cvc_debug_gradient)) {
debug_gradients(group1);
debug_gradients(group2);
debug_gradients(group3);
@ -112,15 +101,15 @@ void colvar::angle::calc_force_invgrads()
// when propagating changes in the angle)
if (b_1site_force) {
group1.read_system_forces();
group1->read_system_forces();
cvm::real norm_fact = 1.0 / dxdr1.norm2();
ft.real_value = norm_fact * dxdr1 * group1.system_force();
ft.real_value = norm_fact * dxdr1 * group1->system_force();
} else {
group1.read_system_forces();
group3.read_system_forces();
group1->read_system_forces();
group3->read_system_forces();
cvm::real norm_fact = 1.0 / (dxdr1.norm2() + dxdr3.norm2());
ft.real_value = norm_fact * ( dxdr1 * group1.system_force()
+ dxdr3 * group3.system_force());
ft.real_value = norm_fact * ( dxdr1 * group1->system_force()
+ dxdr3 * group3->system_force());
}
return;
}
@ -136,14 +125,14 @@ void colvar::angle::calc_Jacobian_derivative()
void colvar::angle::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);
if (!group3.noforce)
group3.apply_colvar_force(force.real_value);
if (!group3->noforce)
group3->apply_colvar_force(force.real_value);
}
@ -153,13 +142,10 @@ colvar::dipole_angle::dipole_angle(std::string const &conf)
: cvc(conf)
{
function_type = "dipole_angle";
parse_group(conf, "group1", group1);
parse_group(conf, "group2", group2);
parse_group(conf, "group3", group3);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3");
atom_groups.push_back(&group1);
atom_groups.push_back(&group2);
atom_groups.push_back(&group3);
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing system force on group 1 only");
}
@ -170,15 +156,16 @@ colvar::dipole_angle::dipole_angle(std::string const &conf)
colvar::dipole_angle::dipole_angle(cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3)
: group1(std::vector<cvm::atom>(1, a1)),
group2(std::vector<cvm::atom>(1, a2)),
group3(std::vector<cvm::atom>(1, a3))
{
function_type = "dipole_angle";
b_1site_force = false;
atom_groups.push_back(&group1);
atom_groups.push_back(&group2);
atom_groups.push_back(&group3);
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
group3 = new cvm::atom_group(std::vector<cvm::atom>(1, a3));
atom_groups.push_back(group1);
atom_groups.push_back(group2);
atom_groups.push_back(group3);
x.type(colvarvalue::type_scalar);
}
@ -193,13 +180,13 @@ colvar::dipole_angle::dipole_angle()
void colvar::dipole_angle::calc_value()
{
cvm::atom_pos const g1_pos = group1.center_of_mass();
cvm::atom_pos const g2_pos = group2.center_of_mass();
cvm::atom_pos const g3_pos = group3.center_of_mass();
cvm::atom_pos const g1_pos = group1->center_of_mass();
cvm::atom_pos const g2_pos = group2->center_of_mass();
cvm::atom_pos const g3_pos = group3->center_of_mass();
group1.calc_dipole(g1_pos);
group1->calc_dipole(g1_pos);
r21 = group1.dipole();
r21 = group1->dipole();
r21l = r21.norm();
r23 = cvm::position_distance(g2_pos, g3_pos);
r23l = r23.norm();
@ -225,35 +212,35 @@ void colvar::dipole_angle::calc_gradients()
(1.0/r23l) * ( r21/r21l + (-1.0) * cos_theta * r23/r23l );
//this auxiliar variables are to avoid numerical errors inside "for"
double aux1 = group1.total_charge/group1.total_mass;
// double aux2 = group2.total_charge/group2.total_mass;
// double aux3 = group3.total_charge/group3.total_mass;
double aux1 = group1->total_charge/group1->total_mass;
// double aux2 = group2->total_charge/group2->total_mass;
// double aux3 = group3->total_charge/group3->total_mass;
size_t i;
for (i = 0; i < group1.size(); i++) {
group1[i].grad =(group1[i].charge + (-1)* group1[i].mass * aux1) * (dxdr1);
for (i = 0; i < group1->size(); i++) {
(*group1)[i].grad =((*group1)[i].charge + (-1)* (*group1)[i].mass * aux1) * (dxdr1);
}
for (i = 0; i < group2.size(); i++) {
group2[i].grad = (group2[i].mass/group2.total_mass)* dxdr3 * (-1.0);
for (i = 0; i < group2->size(); i++) {
(*group2)[i].grad = ((*group2)[i].mass/group2->total_mass)* dxdr3 * (-1.0);
}
for (i = 0; i < group3.size(); i++) {
group3[i].grad =(group3[i].mass/group3.total_mass) * (dxdr3);
for (i = 0; i < group3->size(); i++) {
(*group3)[i].grad =((*group3)[i].mass/group3->total_mass) * (dxdr3);
}
}
void colvar::dipole_angle::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);
if (!group3.noforce)
group3.apply_colvar_force(force.real_value);
if (!group3->noforce)
group3->apply_colvar_force(force.real_value);
}
@ -265,32 +252,26 @@ colvar::dihedral::dihedral(std::string const &conf)
function_type = "dihedral";
period = 360.0;
b_periodic = true;
b_inverse_gradients = true;
b_Jacobian_derivative = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing system force on group 1 only");
}
parse_group(conf, "group1", group1);
parse_group(conf, "group2", group2);
parse_group(conf, "group3", group3);
parse_group(conf, "group4", group4);
atom_groups.push_back(&group1);
atom_groups.push_back(&group2);
atom_groups.push_back(&group3);
atom_groups.push_back(&group4);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3");
group4 = parse_group(conf, "group4");
x.type(colvarvalue::type_scalar);
}
colvar::dihedral::dihedral(cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3,
cvm::atom const &a4)
: group1(std::vector<cvm::atom>(1, a1)),
group2(std::vector<cvm::atom>(1, a2)),
group3(std::vector<cvm::atom>(1, a3)),
group4(std::vector<cvm::atom>(1, a4))
cvm::atom const &a2,
cvm::atom const &a3,
cvm::atom const &a4)
{
if (cvm::debug())
cvm::log("Initializing dihedral object from atom groups.\n");
@ -298,14 +279,20 @@ colvar::dihedral::dihedral(cvm::atom const &a1,
function_type = "dihedral";
period = 360.0;
b_periodic = true;
b_inverse_gradients = true;
b_Jacobian_derivative = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
b_1site_force = false;
atom_groups.push_back(&group1);
atom_groups.push_back(&group2);
atom_groups.push_back(&group3);
atom_groups.push_back(&group4);
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
group3 = new cvm::atom_group(std::vector<cvm::atom>(1, a3));
group4 = new cvm::atom_group(std::vector<cvm::atom>(1, a4));
atom_groups.push_back(group1);
atom_groups.push_back(group2);
atom_groups.push_back(group3);
atom_groups.push_back(group4);
x.type(colvarvalue::type_scalar);
@ -319,18 +306,18 @@ colvar::dihedral::dihedral()
function_type = "dihedral";
period = 360.0;
b_periodic = true;
b_inverse_gradients = true;
b_Jacobian_derivative = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
x.type(colvarvalue::type_scalar);
}
void colvar::dihedral::calc_value()
{
cvm::atom_pos const g1_pos = group1.center_of_mass();
cvm::atom_pos const g2_pos = group2.center_of_mass();
cvm::atom_pos const g3_pos = group3.center_of_mass();
cvm::atom_pos const g4_pos = group4.center_of_mass();
cvm::atom_pos const g1_pos = group1->center_of_mass();
cvm::atom_pos const g2_pos = group2->center_of_mass();
cvm::atom_pos const g3_pos = group3->center_of_mass();
cvm::atom_pos const g4_pos = group4->center_of_mass();
// Usual sign convention: r12 = r2 - r1
r12 = cvm::position_distance(g1_pos, g2_pos);
@ -415,18 +402,10 @@ void colvar::dihedral::calc_gradients()
+dsindB.y*r34.x - dsindB.x*r34.y);
}
size_t i;
for (i = 0; i < group1.size(); i++)
group1[i].grad = (group1[i].mass/group1.total_mass) * (-f1);
for (i = 0; i < group2.size(); i++)
group2[i].grad = (group2[i].mass/group2.total_mass) * (-f2 + f1);
for (i = 0; i < group3.size(); i++)
group3[i].grad = (group3[i].mass/group3.total_mass) * (-f3 + f2);
for (i = 0; i < group4.size(); i++)
group4[i].grad = (group4[i].mass/group4.total_mass) * (f3);
group1->set_weighted_gradient(-f1);
group2->set_weighted_gradient(-f2 + f1);
group3->set_weighted_gradient(-f3 + f2);
group4->set_weighted_gradient(f3);
}
@ -448,15 +427,15 @@ void colvar::dihedral::calc_force_invgrads()
cvm::real const fact1 = d12 * std::sqrt(1.0 - dot1 * dot1);
cvm::real const fact4 = d34 * std::sqrt(1.0 - dot4 * dot4);
group1.read_system_forces();
group1->read_system_forces();
if ( b_1site_force ) {
// This is only measuring the force on group 1
ft.real_value = PI/180.0 * fact1 * (cross1 * group1.system_force());
ft.real_value = PI/180.0 * fact1 * (cross1 * group1->system_force());
} else {
// Default case: use groups 1 and 4
group4.read_system_forces();
ft.real_value = PI/180.0 * 0.5 * (fact1 * (cross1 * group1.system_force())
+ fact4 * (cross4 * group4.system_force()));
group4->read_system_forces();
ft.real_value = PI/180.0 * 0.5 * (fact1 * (cross1 * group1->system_force())
+ fact4 * (cross4 * group4->system_force()));
}
}
@ -470,17 +449,17 @@ void colvar::dihedral::calc_Jacobian_derivative()
void colvar::dihedral::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);
if (!group3.noforce)
group3.apply_colvar_force(force.real_value);
if (!group3->noforce)
group3->apply_colvar_force(force.real_value);
if (!group4.noforce)
group4.apply_colvar_force(force.real_value);
if (!group4->noforce)
group4->apply_colvar_force(force.real_value);
}