git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10118 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -113,7 +113,7 @@ void colvar::distance_vec::calc_value()
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}
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void colvar::distance_vec::calc_gradients()
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{
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{
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// gradients are not stored: a 3x3 matrix for each atom would be
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// needed to store just the identity matrix
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}
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@ -140,7 +140,7 @@ colvar::distance_z::distance_z (std::string const &conf)
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// TODO detect PBC from MD engine (in simple cases)
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// and then update period in real time
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if (period != 0.0)
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b_periodic = true;
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b_periodic = true;
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if ((wrap_center != 0.0) && (period == 0.0)) {
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cvm::fatal_error ("Error: wrapAround was defined in a distanceZ component,"
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@ -153,7 +153,7 @@ colvar::distance_z::distance_z (std::string const &conf)
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atom_groups.push_back (&ref1);
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// this group is optional
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parse_group (conf, "ref2", ref2, true);
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if (ref2.size()) {
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atom_groups.push_back (&ref2);
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cvm::log ("Using axis joining the centers of mass of groups \"ref\" and \"ref2\"");
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@ -522,7 +522,7 @@ colvar::gyration::gyration (std::string const &conf)
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cvm::log ("WARNING: explicit fitting parameters were provided for atom group \"atoms\".");
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} else {
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atoms.b_center = true;
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atoms.ref_pos.assign (1, cvm::rvector (0.0, 0.0, 0.0));
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atoms.ref_pos.assign (1, cvm::atom_pos (0.0, 0.0, 0.0));
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}
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x.type (colvarvalue::type_scalar);
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@ -700,7 +700,7 @@ colvar::rmsd::rmsd (std::string const &conf)
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parse_group (conf, "atoms", atoms);
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atom_groups.push_back (&atoms);
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if (atoms.b_dummy)
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if (atoms.b_dummy)
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cvm::fatal_error ("Error: \"atoms\" cannot be a dummy atom.");
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if (atoms.ref_pos_group != NULL) {
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@ -732,7 +732,7 @@ colvar::rmsd::rmsd (std::string const &conf)
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std::string ref_pos_col;
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double ref_pos_col_value;
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if (get_keyval (conf, "refPositionsCol", ref_pos_col, std::string (""))) {
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// if provided, use PDB column to select coordinates
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bool found = get_keyval (conf, "refPositionsColValue", ref_pos_col_value, 0.0);
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@ -771,7 +771,7 @@ colvar::rmsd::rmsd (std::string const &conf)
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}
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}
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void colvar::rmsd::calc_value()
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{
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// rotational-translational fit is handled by the atom group
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@ -813,9 +813,9 @@ void colvar::rmsd::calc_force_invgrads()
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{
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atoms.read_system_forces();
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ft.real_value = 0.0;
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// Note: gradient square norm is 1/N_atoms
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for (size_t ia = 0; ia < atoms.size(); ia++) {
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ft.real_value += atoms[ia].grad * atoms[ia].system_force;
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}
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@ -832,7 +832,7 @@ void colvar::rmsd::calc_Jacobian_derivative()
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// gradient of the rotation matrix
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cvm::matrix2d <cvm::rvector, 3, 3> grad_rot_mat;
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// gradients of products of 2 quaternion components
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// gradients of products of 2 quaternion components
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cvm::rvector g11, g22, g33, g01, g02, g03, g12, g13, g23;
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for (size_t ia = 0; ia < atoms.size(); ia++) {
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@ -850,15 +850,15 @@ void colvar::rmsd::calc_Jacobian_derivative()
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g23 = (atoms.rot.q)[2]*dq[3] + (atoms.rot.q)[3]*dq[2];
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// Gradient of the rotation matrix wrt current Cartesian position
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grad_rot_mat[0][0] = -2.0 * (g22 + g33);
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grad_rot_mat[1][0] = 2.0 * (g12 + g03);
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grad_rot_mat[2][0] = 2.0 * (g13 - g02);
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grad_rot_mat[0][1] = 2.0 * (g12 - g03);
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grad_rot_mat[1][1] = -2.0 * (g11 + g33);
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grad_rot_mat[2][1] = 2.0 * (g01 + g23);
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grad_rot_mat[0][2] = 2.0 * (g02 + g13);
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grad_rot_mat[1][2] = 2.0 * (g23 - g01);
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grad_rot_mat[2][2] = -2.0 * (g11 + g22);
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grad_rot_mat[0][0] = -2.0 * (g22 + g33);
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grad_rot_mat[1][0] = 2.0 * (g12 + g03);
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grad_rot_mat[2][0] = 2.0 * (g13 - g02);
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grad_rot_mat[0][1] = 2.0 * (g12 - g03);
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grad_rot_mat[1][1] = -2.0 * (g11 + g33);
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grad_rot_mat[2][1] = 2.0 * (g01 + g23);
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grad_rot_mat[0][2] = 2.0 * (g02 + g13);
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grad_rot_mat[1][2] = 2.0 * (g23 - g01);
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grad_rot_mat[2][2] = -2.0 * (g11 + g22);
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cvm::atom_pos &y = ref_pos[ia];
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@ -991,7 +991,7 @@ colvar::eigenvector::eigenvector (std::string const &conf)
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"and eigenvector must be defined.\n");
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}
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cvm::rvector eig_center (0.0, 0.0, 0.0);
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cvm::atom_pos eig_center (0.0, 0.0, 0.0);
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for (size_t i = 0; i < atoms.size(); i++) {
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eig_center += eigenvec[i];
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}
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@ -1053,7 +1053,7 @@ colvar::eigenvector::eigenvector (std::string const &conf)
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}
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}
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void colvar::eigenvector::calc_value()
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{
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x.real_value = 0.0;
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@ -1087,7 +1087,7 @@ void colvar::eigenvector::calc_force_invgrads()
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{
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atoms.read_system_forces();
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ft.real_value = 0.0;
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for (size_t ia = 0; ia < atoms.size(); ia++) {
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ft.real_value += eigenvec_invnorm2 * atoms[ia].grad *
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atoms[ia].system_force;
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@ -1101,10 +1101,10 @@ void colvar::eigenvector::calc_Jacobian_derivative()
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cvm::matrix2d <cvm::rvector, 3, 3> grad_rot_mat;
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cvm::quaternion &quat0 = atoms.rot.q;
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// gradients of products of 2 quaternion components
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// gradients of products of 2 quaternion components
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cvm::rvector g11, g22, g33, g01, g02, g03, g12, g13, g23;
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cvm::atom_pos x_relative;
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cvm::atom_pos x_relative;
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cvm::real sum = 0.0;
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for (size_t ia = 0; ia < atoms.size(); ia++) {
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@ -1126,15 +1126,15 @@ void colvar::eigenvector::calc_Jacobian_derivative()
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// Gradient of the inverse rotation matrix wrt current Cartesian position
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// (transpose of the gradient of the direct rotation)
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grad_rot_mat[0][0] = -2.0 * (g22 + g33);
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grad_rot_mat[0][1] = 2.0 * (g12 + g03);
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grad_rot_mat[0][2] = 2.0 * (g13 - g02);
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grad_rot_mat[1][0] = 2.0 * (g12 - g03);
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grad_rot_mat[1][1] = -2.0 * (g11 + g33);
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grad_rot_mat[1][2] = 2.0 * (g01 + g23);
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grad_rot_mat[2][0] = 2.0 * (g02 + g13);
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grad_rot_mat[2][1] = 2.0 * (g23 - g01);
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grad_rot_mat[2][2] = -2.0 * (g11 + g22);
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grad_rot_mat[0][0] = -2.0 * (g22 + g33);
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grad_rot_mat[0][1] = 2.0 * (g12 + g03);
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grad_rot_mat[0][2] = 2.0 * (g13 - g02);
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grad_rot_mat[1][0] = 2.0 * (g12 - g03);
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grad_rot_mat[1][1] = -2.0 * (g11 + g33);
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grad_rot_mat[1][2] = 2.0 * (g01 + g23);
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grad_rot_mat[2][0] = 2.0 * (g02 + g13);
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grad_rot_mat[2][1] = 2.0 * (g23 - g01);
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grad_rot_mat[2][2] = -2.0 * (g11 + g22);
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for (size_t i = 0; i < 3; i++) {
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for (size_t j = 0; j < 3; j++) {
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@ -1143,7 +1143,7 @@ void colvar::eigenvector::calc_Jacobian_derivative()
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}
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}
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jd.real_value = sum * std::sqrt (eigenvec_invnorm2);
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jd.real_value = sum * std::sqrt (eigenvec_invnorm2);
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}
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