[cee0b57] | 1 | /*
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| 2 | * molecule_geometry.cpp
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| 3 | *
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| 4 | * Created on: Oct 5, 2009
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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[aafd77] | 8 | #ifdef HAVE_CONFIG_H
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| 9 | #include <config.h>
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| 10 | #endif
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| 11 |
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[112b09] | 12 | #include "Helpers/MemDebug.hpp"
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| 13 |
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[f66195] | 14 | #include "atom.hpp"
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| 15 | #include "bond.hpp"
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[cee0b57] | 16 | #include "config.hpp"
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[f66195] | 17 | #include "element.hpp"
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| 18 | #include "helpers.hpp"
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| 19 | #include "leastsquaremin.hpp"
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[36166d] | 20 | #include "verbose.hpp"
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[e138de] | 21 | #include "log.hpp"
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[cee0b57] | 22 | #include "molecule.hpp"
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[b34306] | 23 | #include "World.hpp"
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[ccf826] | 24 | #include "Plane.hpp"
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[c94eeb] | 25 | #include "Matrix.hpp"
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[84c494] | 26 | #include "Box.hpp"
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[76c0d6] | 27 | #include <boost/foreach.hpp>
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| 28 |
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[aafd77] | 29 | #include <gsl/gsl_eigen.h>
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| 30 | #include <gsl/gsl_multimin.h>
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| 31 |
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[cee0b57] | 32 |
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| 33 | /************************************* Functions for class molecule *********************************/
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| 34 |
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| 35 |
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| 36 | /** Centers the molecule in the box whose lengths are defined by vector \a *BoxLengths.
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| 37 | * \param *out output stream for debugging
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| 38 | */
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[e138de] | 39 | bool molecule::CenterInBox()
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[cee0b57] | 40 | {
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| 41 | bool status = true;
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[e138de] | 42 | const Vector *Center = DetermineCenterOfAll();
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[eddea2] | 43 | const Vector *CenterBox = DetermineCenterOfBox();
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[f429d7] | 44 | Box &domain = World::getInstance().getDomain();
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[cee0b57] | 45 |
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| 46 | // go through all atoms
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[273382] | 47 | ActOnAllVectors( &Vector::SubtractVector, *Center);
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[eddea2] | 48 | ActOnAllVectors( &Vector::SubtractVector, *CenterBox);
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[d0f111] | 49 | BOOST_FOREACH(atom* iter, atoms){
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[f429d7] | 50 | *iter->node = domain.WrapPeriodically(*iter->node);
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[d0f111] | 51 | }
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[cee0b57] | 52 |
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| 53 | delete(Center);
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[52d777] | 54 | delete(CenterBox);
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[cee0b57] | 55 | return status;
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| 56 | };
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| 57 |
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| 58 |
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| 59 | /** Bounds the molecule in the box whose lengths are defined by vector \a *BoxLengths.
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| 60 | * \param *out output stream for debugging
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| 61 | */
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[e138de] | 62 | bool molecule::BoundInBox()
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[cee0b57] | 63 | {
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| 64 | bool status = true;
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[f429d7] | 65 | Box &domain = World::getInstance().getDomain();
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[cee0b57] | 66 |
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| 67 | // go through all atoms
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[d0f111] | 68 | BOOST_FOREACH(atom* iter, atoms){
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[f429d7] | 69 | *iter->node = domain.WrapPeriodically(*iter->node);
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[d0f111] | 70 | }
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[cee0b57] | 71 |
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| 72 | return status;
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| 73 | };
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| 74 |
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| 75 | /** Centers the edge of the atoms at (0,0,0).
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| 76 | * \param *out output stream for debugging
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| 77 | * \param *max coordinates of other edge, specifying box dimensions.
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| 78 | */
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[e138de] | 79 | void molecule::CenterEdge(Vector *max)
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[cee0b57] | 80 | {
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| 81 | Vector *min = new Vector;
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| 82 |
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[e138de] | 83 | // Log() << Verbose(3) << "Begin of CenterEdge." << endl;
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[9879f6] | 84 | molecule::const_iterator iter = begin(); // start at first in list
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| 85 | if (iter != end()) { //list not empty?
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[cee0b57] | 86 | for (int i=NDIM;i--;) {
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[a7b761b] | 87 | max->at(i) = (*iter)->x[i];
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| 88 | min->at(i) = (*iter)->x[i];
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[cee0b57] | 89 | }
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[9879f6] | 90 | for (; iter != end(); ++iter) {// continue with second if present
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| 91 | //(*iter)->Output(1,1,out);
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[cee0b57] | 92 | for (int i=NDIM;i--;) {
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[a7b761b] | 93 | max->at(i) = (max->at(i) < (*iter)->x[i]) ? (*iter)->x[i] : max->at(i);
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| 94 | min->at(i) = (min->at(i) > (*iter)->x[i]) ? (*iter)->x[i] : min->at(i);
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[cee0b57] | 95 | }
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| 96 | }
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[e138de] | 97 | // Log() << Verbose(4) << "Maximum is ";
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[cee0b57] | 98 | // max->Output(out);
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[e138de] | 99 | // Log() << Verbose(0) << ", Minimum is ";
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[cee0b57] | 100 | // min->Output(out);
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[e138de] | 101 | // Log() << Verbose(0) << endl;
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[cee0b57] | 102 | min->Scale(-1.);
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[273382] | 103 | (*max) += (*min);
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[cee0b57] | 104 | Translate(min);
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| 105 | Center.Zero();
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| 106 | }
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| 107 | delete(min);
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[e138de] | 108 | // Log() << Verbose(3) << "End of CenterEdge." << endl;
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[cee0b57] | 109 | };
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| 110 |
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| 111 | /** Centers the center of the atoms at (0,0,0).
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| 112 | * \param *out output stream for debugging
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| 113 | * \param *center return vector for translation vector
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| 114 | */
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[e138de] | 115 | void molecule::CenterOrigin()
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[cee0b57] | 116 | {
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| 117 | int Num = 0;
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[9879f6] | 118 | molecule::const_iterator iter = begin(); // start at first in list
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[cee0b57] | 119 |
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| 120 | Center.Zero();
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| 121 |
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[9879f6] | 122 | if (iter != end()) { //list not empty?
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| 123 | for (; iter != end(); ++iter) { // continue with second if present
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[cee0b57] | 124 | Num++;
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[a7b761b] | 125 | Center += (*iter)->x;
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[cee0b57] | 126 | }
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[bdc91e] | 127 | Center.Scale(-1./(double)Num); // divide through total number (and sign for direction)
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[cee0b57] | 128 | Translate(&Center);
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| 129 | Center.Zero();
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| 130 | }
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| 131 | };
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| 132 |
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| 133 | /** Returns vector pointing to center of all atoms.
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| 134 | * \return pointer to center of all vector
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| 135 | */
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[e138de] | 136 | Vector * molecule::DetermineCenterOfAll() const
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[cee0b57] | 137 | {
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[9879f6] | 138 | molecule::const_iterator iter = begin(); // start at first in list
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[cee0b57] | 139 | Vector *a = new Vector();
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| 140 | double Num = 0;
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| 141 |
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| 142 | a->Zero();
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| 143 |
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[9879f6] | 144 | if (iter != end()) { //list not empty?
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| 145 | for (; iter != end(); ++iter) { // continue with second if present
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[15b670] | 146 | Num++;
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[1024cb] | 147 | (*a) += (*iter)->x;
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[cee0b57] | 148 | }
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[bdc91e] | 149 | a->Scale(1./(double)Num); // divide through total mass (and sign for direction)
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[cee0b57] | 150 | }
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| 151 | return a;
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| 152 | };
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| 153 |
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[eddea2] | 154 | /** Returns vector pointing to center of the domain.
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| 155 | * \return pointer to center of the domain
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| 156 | */
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| 157 | Vector * molecule::DetermineCenterOfBox() const
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| 158 | {
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| 159 | Vector *a = new Vector(0.5,0.5,0.5);
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[84c494] | 160 | const Matrix &M = World::getInstance().getDomain().getM();
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[5108e1] | 161 | (*a) *= M;
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[eddea2] | 162 | return a;
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| 163 | };
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| 164 |
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[cee0b57] | 165 | /** Returns vector pointing to center of gravity.
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| 166 | * \param *out output stream for debugging
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| 167 | * \return pointer to center of gravity vector
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| 168 | */
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[e138de] | 169 | Vector * molecule::DetermineCenterOfGravity()
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[cee0b57] | 170 | {
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[9879f6] | 171 | molecule::const_iterator iter = begin(); // start at first in list
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[cee0b57] | 172 | Vector *a = new Vector();
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| 173 | Vector tmp;
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| 174 | double Num = 0;
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| 175 |
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| 176 | a->Zero();
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| 177 |
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[9879f6] | 178 | if (iter != end()) { //list not empty?
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| 179 | for (; iter != end(); ++iter) { // continue with second if present
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| 180 | Num += (*iter)->type->mass;
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[a7b761b] | 181 | tmp = (*iter)->type->mass * (*iter)->x;
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[273382] | 182 | (*a) += tmp;
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[cee0b57] | 183 | }
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[bdc91e] | 184 | a->Scale(1./Num); // divide through total mass
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[cee0b57] | 185 | }
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[e138de] | 186 | // Log() << Verbose(1) << "Resulting center of gravity: ";
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[cee0b57] | 187 | // a->Output(out);
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[e138de] | 188 | // Log() << Verbose(0) << endl;
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[cee0b57] | 189 | return a;
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| 190 | };
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| 191 |
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| 192 | /** Centers the center of gravity of the atoms at (0,0,0).
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| 193 | * \param *out output stream for debugging
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| 194 | * \param *center return vector for translation vector
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| 195 | */
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[e138de] | 196 | void molecule::CenterPeriodic()
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[cee0b57] | 197 | {
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| 198 | DeterminePeriodicCenter(Center);
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| 199 | };
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| 200 |
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| 201 |
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| 202 | /** Centers the center of gravity of the atoms at (0,0,0).
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| 203 | * \param *out output stream for debugging
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| 204 | * \param *center return vector for translation vector
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| 205 | */
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[e138de] | 206 | void molecule::CenterAtVector(Vector *newcenter)
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[cee0b57] | 207 | {
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[273382] | 208 | Center = *newcenter;
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[cee0b57] | 209 | };
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| 210 |
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| 211 |
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| 212 | /** Scales all atoms by \a *factor.
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| 213 | * \param *factor pointer to scaling factor
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[1bd79e] | 214 | *
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| 215 | * TODO: Is this realy what is meant, i.e.
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| 216 | * x=(x[0]*factor[0],x[1]*factor[1],x[2]*factor[2]) (current impl)
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| 217 | * or rather
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| 218 | * x=(**factor) * x (as suggested by comment)
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[cee0b57] | 219 | */
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[776b64] | 220 | void molecule::Scale(const double ** const factor)
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[cee0b57] | 221 | {
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[9879f6] | 222 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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[cee0b57] | 223 | for (int j=0;j<MDSteps;j++)
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[a7b761b] | 224 | (*iter)->Trajectory.R.at(j).ScaleAll(*factor);
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| 225 | (*iter)->x.ScaleAll(*factor);
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[cee0b57] | 226 | }
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| 227 | };
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| 228 |
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| 229 | /** Translate all atoms by given vector.
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| 230 | * \param trans[] translation vector.
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| 231 | */
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| 232 | void molecule::Translate(const Vector *trans)
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| 233 | {
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[9879f6] | 234 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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[cee0b57] | 235 | for (int j=0;j<MDSteps;j++)
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[a7b761b] | 236 | (*iter)->Trajectory.R.at(j) += (*trans);
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| 237 | (*iter)->x += (*trans);
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[cee0b57] | 238 | }
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| 239 | };
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| 240 |
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| 241 | /** Translate the molecule periodically in the box.
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| 242 | * \param trans[] translation vector.
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| 243 | * TODO treatment of trajetories missing
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| 244 | */
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| 245 | void molecule::TranslatePeriodically(const Vector *trans)
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| 246 | {
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[f429d7] | 247 | Box &domain = World::getInstance().getDomain();
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[cee0b57] | 248 |
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| 249 | // go through all atoms
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[eddea2] | 250 | ActOnAllVectors( &Vector::AddVector, *trans);
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[d0f111] | 251 | BOOST_FOREACH(atom* iter, atoms){
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[f429d7] | 252 | *iter->node = domain.WrapPeriodically(*iter->node);
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[d0f111] | 253 | }
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[cee0b57] | 254 |
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| 255 | };
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| 256 |
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| 257 |
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| 258 | /** Mirrors all atoms against a given plane.
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| 259 | * \param n[] normal vector of mirror plane.
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| 260 | */
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| 261 | void molecule::Mirror(const Vector *n)
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| 262 | {
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[76c0d6] | 263 | OBSERVE;
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[ccf826] | 264 | Plane p(*n,0);
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[d0f111] | 265 | BOOST_FOREACH(atom* iter, atoms ){
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[76c0d6] | 266 | (*iter->node) = p.mirrorVector(*iter->node);
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[ccf826] | 267 | }
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[cee0b57] | 268 | };
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| 269 |
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| 270 | /** Determines center of molecule (yet not considering atom masses).
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| 271 | * \param center reference to return vector
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| 272 | */
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| 273 | void molecule::DeterminePeriodicCenter(Vector ¢er)
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| 274 | {
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[84c494] | 275 | const Matrix &matrix = World::getInstance().getDomain().getM();
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| 276 | const Matrix &inversematrix = World::getInstance().getDomain().getM();
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[cee0b57] | 277 | double tmp;
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| 278 | bool flag;
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| 279 | Vector Testvector, Translationvector;
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| 280 |
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| 281 | do {
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| 282 | Center.Zero();
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| 283 | flag = true;
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[9879f6] | 284 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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[cee0b57] | 285 | #ifdef ADDHYDROGEN
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[9879f6] | 286 | if ((*iter)->type->Z != 1) {
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[cee0b57] | 287 | #endif
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[5108e1] | 288 | Testvector = inversematrix * (*iter)->x;
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[cee0b57] | 289 | Translationvector.Zero();
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[9879f6] | 290 | for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
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| 291 | if ((*iter)->nr < (*Runner)->GetOtherAtom((*iter))->nr) // otherwise we shift one to, the other fro and gain nothing
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[cee0b57] | 292 | for (int j=0;j<NDIM;j++) {
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[a7b761b] | 293 | tmp = (*iter)->x[j] - (*Runner)->GetOtherAtom(*iter)->x[j];
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[cee0b57] | 294 | if ((fabs(tmp)) > BondDistance) {
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| 295 | flag = false;
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[a7b761b] | 296 | DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << (*iter)->getName() << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);
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[cee0b57] | 297 | if (tmp > 0)
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[0a4f7f] | 298 | Translationvector[j] -= 1.;
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[cee0b57] | 299 | else
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[0a4f7f] | 300 | Translationvector[j] += 1.;
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[cee0b57] | 301 | }
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| 302 | }
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| 303 | }
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[273382] | 304 | Testvector += Translationvector;
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[5108e1] | 305 | Testvector *= matrix;
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[273382] | 306 | Center += Testvector;
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[0a4f7f] | 307 | Log() << Verbose(1) << "vector is: " << Testvector << endl;
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[cee0b57] | 308 | #ifdef ADDHYDROGEN
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| 309 | // now also change all hydrogens
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[9879f6] | 310 | for (BondList::const_iterator Runner = (*iter)->ListOfBonds.begin(); Runner != (*iter)->ListOfBonds.end(); (++Runner)) {
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| 311 | if ((*Runner)->GetOtherAtom((*iter))->type->Z == 1) {
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[5108e1] | 312 | Testvector = inversematrix * (*Runner)->GetOtherAtom((*iter))->x;
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[273382] | 313 | Testvector += Translationvector;
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[5108e1] | 314 | Testvector *= matrix;
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[273382] | 315 | Center += Testvector;
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[0a4f7f] | 316 | Log() << Verbose(1) << "Hydrogen vector is: " << Testvector << endl;
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[cee0b57] | 317 | }
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| 318 | }
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| 319 | }
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| 320 | #endif
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| 321 | }
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| 322 | } while (!flag);
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[1614174] | 323 |
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[ea7176] | 324 | Center.Scale(1./static_cast<double>(getAtomCount()));
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[cee0b57] | 325 | };
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| 326 |
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| 327 | /** Transforms/Rotates the given molecule into its principal axis system.
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| 328 | * \param *out output stream for debugging
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| 329 | * \param DoRotate whether to rotate (true) or only to determine the PAS.
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| 330 | * TODO treatment of trajetories missing
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| 331 | */
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[e138de] | 332 | void molecule::PrincipalAxisSystem(bool DoRotate)
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[cee0b57] | 333 | {
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| 334 | double InertiaTensor[NDIM*NDIM];
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[e138de] | 335 | Vector *CenterOfGravity = DetermineCenterOfGravity();
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[cee0b57] | 336 |
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[e138de] | 337 | CenterPeriodic();
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[cee0b57] | 338 |
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| 339 | // reset inertia tensor
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| 340 | for(int i=0;i<NDIM*NDIM;i++)
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| 341 | InertiaTensor[i] = 0.;
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| 342 |
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| 343 | // sum up inertia tensor
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[9879f6] | 344 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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[a7b761b] | 345 | Vector x = (*iter)->x;
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[cee0b57] | 346 | //x.SubtractVector(CenterOfGravity);
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[a7b761b] | 347 | InertiaTensor[0] += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
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| 348 | InertiaTensor[1] += (*iter)->type->mass*(-x[0]*x[1]);
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| 349 | InertiaTensor[2] += (*iter)->type->mass*(-x[0]*x[2]);
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| 350 | InertiaTensor[3] += (*iter)->type->mass*(-x[1]*x[0]);
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| 351 | InertiaTensor[4] += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
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| 352 | InertiaTensor[5] += (*iter)->type->mass*(-x[1]*x[2]);
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| 353 | InertiaTensor[6] += (*iter)->type->mass*(-x[2]*x[0]);
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| 354 | InertiaTensor[7] += (*iter)->type->mass*(-x[2]*x[1]);
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| 355 | InertiaTensor[8] += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
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[cee0b57] | 356 | }
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| 357 | // print InertiaTensor for debugging
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[a67d19] | 358 | DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << endl);
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[cee0b57] | 359 | for(int i=0;i<NDIM;i++) {
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| 360 | for(int j=0;j<NDIM;j++)
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[a67d19] | 361 | DoLog(0) && (Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ");
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| 362 | DoLog(0) && (Log() << Verbose(0) << endl);
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[cee0b57] | 363 | }
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[a67d19] | 364 | DoLog(0) && (Log() << Verbose(0) << endl);
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[cee0b57] | 365 |
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| 366 | // diagonalize to determine principal axis system
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| 367 | gsl_eigen_symmv_workspace *T = gsl_eigen_symmv_alloc(NDIM);
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| 368 | gsl_matrix_view m = gsl_matrix_view_array(InertiaTensor, NDIM, NDIM);
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| 369 | gsl_vector *eval = gsl_vector_alloc(NDIM);
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| 370 | gsl_matrix *evec = gsl_matrix_alloc(NDIM, NDIM);
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| 371 | gsl_eigen_symmv(&m.matrix, eval, evec, T);
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| 372 | gsl_eigen_symmv_free(T);
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| 373 | gsl_eigen_symmv_sort(eval, evec, GSL_EIGEN_SORT_ABS_DESC);
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| 374 |
|
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| 375 | for(int i=0;i<NDIM;i++) {
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[a67d19] | 376 | DoLog(1) && (Log() << Verbose(1) << "eigenvalue = " << gsl_vector_get(eval, i));
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| 377 | DoLog(0) && (Log() << Verbose(0) << ", eigenvector = (" << evec->data[i * evec->tda + 0] << "," << evec->data[i * evec->tda + 1] << "," << evec->data[i * evec->tda + 2] << ")" << endl);
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[cee0b57] | 378 | }
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| 379 |
|
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| 380 | // check whether we rotate or not
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| 381 | if (DoRotate) {
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[a67d19] | 382 | DoLog(1) && (Log() << Verbose(1) << "Transforming molecule into PAS ... ");
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[cee0b57] | 383 | // the eigenvectors specify the transformation matrix
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[c94eeb] | 384 | Matrix M = Matrix(evec->data);
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[5108e1] | 385 | BOOST_FOREACH(atom* iter, atoms){
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| 386 | (*iter->node) *= M;
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| 387 | }
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[a67d19] | 388 | DoLog(0) && (Log() << Verbose(0) << "done." << endl);
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[cee0b57] | 389 |
|
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| 390 | // summing anew for debugging (resulting matrix has to be diagonal!)
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| 391 | // reset inertia tensor
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| 392 | for(int i=0;i<NDIM*NDIM;i++)
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| 393 | InertiaTensor[i] = 0.;
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| 394 |
|
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| 395 | // sum up inertia tensor
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[9879f6] | 396 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
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[a7b761b] | 397 | Vector x = (*iter)->x;
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| 398 | InertiaTensor[0] += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
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| 399 | InertiaTensor[1] += (*iter)->type->mass*(-x[0]*x[1]);
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| 400 | InertiaTensor[2] += (*iter)->type->mass*(-x[0]*x[2]);
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| 401 | InertiaTensor[3] += (*iter)->type->mass*(-x[1]*x[0]);
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| 402 | InertiaTensor[4] += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
|
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| 403 | InertiaTensor[5] += (*iter)->type->mass*(-x[1]*x[2]);
|
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| 404 | InertiaTensor[6] += (*iter)->type->mass*(-x[2]*x[0]);
|
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| 405 | InertiaTensor[7] += (*iter)->type->mass*(-x[2]*x[1]);
|
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| 406 | InertiaTensor[8] += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
|
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[cee0b57] | 407 | }
|
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| 408 | // print InertiaTensor for debugging
|
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[a67d19] | 409 | DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << endl);
|
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[cee0b57] | 410 | for(int i=0;i<NDIM;i++) {
|
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| 411 | for(int j=0;j<NDIM;j++)
|
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[a67d19] | 412 | DoLog(0) && (Log() << Verbose(0) << InertiaTensor[i*NDIM+j] << " ");
|
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| 413 | DoLog(0) && (Log() << Verbose(0) << endl);
|
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[cee0b57] | 414 | }
|
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[a67d19] | 415 | DoLog(0) && (Log() << Verbose(0) << endl);
|
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[cee0b57] | 416 | }
|
---|
| 417 |
|
---|
| 418 | // free everything
|
---|
| 419 | delete(CenterOfGravity);
|
---|
| 420 | gsl_vector_free(eval);
|
---|
| 421 | gsl_matrix_free(evec);
|
---|
| 422 | };
|
---|
| 423 |
|
---|
| 424 |
|
---|
| 425 | /** Align all atoms in such a manner that given vector \a *n is along z axis.
|
---|
| 426 | * \param n[] alignment vector.
|
---|
| 427 | */
|
---|
| 428 | void molecule::Align(Vector *n)
|
---|
| 429 | {
|
---|
| 430 | double alpha, tmp;
|
---|
| 431 | Vector z_axis;
|
---|
[0a4f7f] | 432 | z_axis[0] = 0.;
|
---|
| 433 | z_axis[1] = 0.;
|
---|
| 434 | z_axis[2] = 1.;
|
---|
[cee0b57] | 435 |
|
---|
| 436 | // rotate on z-x plane
|
---|
[a67d19] | 437 | DoLog(0) && (Log() << Verbose(0) << "Begin of Aligning all atoms." << endl);
|
---|
[0a4f7f] | 438 | alpha = atan(-n->at(0)/n->at(2));
|
---|
[a67d19] | 439 | DoLog(1) && (Log() << Verbose(1) << "Z-X-angle: " << alpha << " ... ");
|
---|
[9879f6] | 440 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
|
---|
[a7b761b] | 441 | tmp = (*iter)->x[0];
|
---|
| 442 | (*iter)->x[0] = cos(alpha) * tmp + sin(alpha) * (*iter)->x[2];
|
---|
| 443 | (*iter)->x[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->x[2];
|
---|
[cee0b57] | 444 | for (int j=0;j<MDSteps;j++) {
|
---|
[a7b761b] | 445 | tmp = (*iter)->Trajectory.R.at(j)[0];
|
---|
| 446 | (*iter)->Trajectory.R.at(j)[0] = cos(alpha) * tmp + sin(alpha) * (*iter)->Trajectory.R.at(j)[2];
|
---|
| 447 | (*iter)->Trajectory.R.at(j)[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->Trajectory.R.at(j)[2];
|
---|
[cee0b57] | 448 | }
|
---|
| 449 | }
|
---|
| 450 | // rotate n vector
|
---|
[0a4f7f] | 451 | tmp = n->at(0);
|
---|
| 452 | n->at(0) = cos(alpha) * tmp + sin(alpha) * n->at(2);
|
---|
| 453 | n->at(2) = -sin(alpha) * tmp + cos(alpha) * n->at(2);
|
---|
[8cbb97] | 454 | DoLog(1) && (Log() << Verbose(1) << "alignment vector after first rotation: " << n << endl);
|
---|
[cee0b57] | 455 |
|
---|
| 456 | // rotate on z-y plane
|
---|
[0a4f7f] | 457 | alpha = atan(-n->at(1)/n->at(2));
|
---|
[a67d19] | 458 | DoLog(1) && (Log() << Verbose(1) << "Z-Y-angle: " << alpha << " ... ");
|
---|
[9879f6] | 459 | for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
|
---|
[a7b761b] | 460 | tmp = (*iter)->x[1];
|
---|
| 461 | (*iter)->x[1] = cos(alpha) * tmp + sin(alpha) * (*iter)->x[2];
|
---|
| 462 | (*iter)->x[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->x[2];
|
---|
[cee0b57] | 463 | for (int j=0;j<MDSteps;j++) {
|
---|
[a7b761b] | 464 | tmp = (*iter)->Trajectory.R.at(j)[1];
|
---|
| 465 | (*iter)->Trajectory.R.at(j)[1] = cos(alpha) * tmp + sin(alpha) * (*iter)->Trajectory.R.at(j)[2];
|
---|
| 466 | (*iter)->Trajectory.R.at(j)[2] = -sin(alpha) * tmp + cos(alpha) * (*iter)->Trajectory.R.at(j)[2];
|
---|
[cee0b57] | 467 | }
|
---|
| 468 | }
|
---|
| 469 | // rotate n vector (for consistency check)
|
---|
[0a4f7f] | 470 | tmp = n->at(1);
|
---|
| 471 | n->at(1) = cos(alpha) * tmp + sin(alpha) * n->at(2);
|
---|
| 472 | n->at(2) = -sin(alpha) * tmp + cos(alpha) * n->at(2);
|
---|
[cee0b57] | 473 |
|
---|
| 474 |
|
---|
[8cbb97] | 475 | DoLog(1) && (Log() << Verbose(1) << "alignment vector after second rotation: " << n << endl);
|
---|
[a67d19] | 476 | DoLog(0) && (Log() << Verbose(0) << "End of Aligning all atoms." << endl);
|
---|
[cee0b57] | 477 | };
|
---|
| 478 |
|
---|
| 479 |
|
---|
| 480 | /** Calculates sum over least square distance to line hidden in \a *x.
|
---|
| 481 | * \param *x offset and direction vector
|
---|
| 482 | * \param *params pointer to lsq_params structure
|
---|
| 483 | * \return \f$ sum_i^N | y_i - (a + t_i b)|^2\f$
|
---|
| 484 | */
|
---|
| 485 | double LeastSquareDistance (const gsl_vector * x, void * params)
|
---|
| 486 | {
|
---|
| 487 | double res = 0, t;
|
---|
| 488 | Vector a,b,c,d;
|
---|
| 489 | struct lsq_params *par = (struct lsq_params *)params;
|
---|
| 490 |
|
---|
| 491 | // initialize vectors
|
---|
[0a4f7f] | 492 | a[0] = gsl_vector_get(x,0);
|
---|
| 493 | a[1] = gsl_vector_get(x,1);
|
---|
| 494 | a[2] = gsl_vector_get(x,2);
|
---|
| 495 | b[0] = gsl_vector_get(x,3);
|
---|
| 496 | b[1] = gsl_vector_get(x,4);
|
---|
| 497 | b[2] = gsl_vector_get(x,5);
|
---|
[cee0b57] | 498 | // go through all atoms
|
---|
[9879f6] | 499 | for (molecule::const_iterator iter = par->mol->begin(); iter != par->mol->end(); ++iter) {
|
---|
| 500 | if ((*iter)->type == ((struct lsq_params *)params)->type) { // for specific type
|
---|
[a7b761b] | 501 | c = (*iter)->x - a;
|
---|
[273382] | 502 | t = c.ScalarProduct(b); // get direction parameter
|
---|
| 503 | d = t*b; // and create vector
|
---|
| 504 | c -= d; // ... yielding distance vector
|
---|
| 505 | res += d.ScalarProduct(d); // add squared distance
|
---|
[cee0b57] | 506 | }
|
---|
| 507 | }
|
---|
| 508 | return res;
|
---|
| 509 | };
|
---|
| 510 |
|
---|
| 511 | /** By minimizing the least square distance gains alignment vector.
|
---|
| 512 | * \bug this is not yet working properly it seems
|
---|
| 513 | */
|
---|
| 514 | void molecule::GetAlignvector(struct lsq_params * par) const
|
---|
| 515 | {
|
---|
| 516 | int np = 6;
|
---|
| 517 |
|
---|
| 518 | const gsl_multimin_fminimizer_type *T =
|
---|
| 519 | gsl_multimin_fminimizer_nmsimplex;
|
---|
| 520 | gsl_multimin_fminimizer *s = NULL;
|
---|
| 521 | gsl_vector *ss;
|
---|
| 522 | gsl_multimin_function minex_func;
|
---|
| 523 |
|
---|
| 524 | size_t iter = 0, i;
|
---|
| 525 | int status;
|
---|
| 526 | double size;
|
---|
| 527 |
|
---|
| 528 | /* Initial vertex size vector */
|
---|
| 529 | ss = gsl_vector_alloc (np);
|
---|
| 530 |
|
---|
| 531 | /* Set all step sizes to 1 */
|
---|
| 532 | gsl_vector_set_all (ss, 1.0);
|
---|
| 533 |
|
---|
| 534 | /* Starting point */
|
---|
| 535 | par->x = gsl_vector_alloc (np);
|
---|
| 536 | par->mol = this;
|
---|
| 537 |
|
---|
| 538 | gsl_vector_set (par->x, 0, 0.0); // offset
|
---|
| 539 | gsl_vector_set (par->x, 1, 0.0);
|
---|
| 540 | gsl_vector_set (par->x, 2, 0.0);
|
---|
| 541 | gsl_vector_set (par->x, 3, 0.0); // direction
|
---|
| 542 | gsl_vector_set (par->x, 4, 0.0);
|
---|
| 543 | gsl_vector_set (par->x, 5, 1.0);
|
---|
| 544 |
|
---|
| 545 | /* Initialize method and iterate */
|
---|
| 546 | minex_func.f = &LeastSquareDistance;
|
---|
| 547 | minex_func.n = np;
|
---|
| 548 | minex_func.params = (void *)par;
|
---|
| 549 |
|
---|
| 550 | s = gsl_multimin_fminimizer_alloc (T, np);
|
---|
| 551 | gsl_multimin_fminimizer_set (s, &minex_func, par->x, ss);
|
---|
| 552 |
|
---|
| 553 | do
|
---|
| 554 | {
|
---|
| 555 | iter++;
|
---|
| 556 | status = gsl_multimin_fminimizer_iterate(s);
|
---|
| 557 |
|
---|
| 558 | if (status)
|
---|
| 559 | break;
|
---|
| 560 |
|
---|
| 561 | size = gsl_multimin_fminimizer_size (s);
|
---|
| 562 | status = gsl_multimin_test_size (size, 1e-2);
|
---|
| 563 |
|
---|
| 564 | if (status == GSL_SUCCESS)
|
---|
| 565 | {
|
---|
| 566 | printf ("converged to minimum at\n");
|
---|
| 567 | }
|
---|
| 568 |
|
---|
| 569 | printf ("%5d ", (int)iter);
|
---|
| 570 | for (i = 0; i < (size_t)np; i++)
|
---|
| 571 | {
|
---|
| 572 | printf ("%10.3e ", gsl_vector_get (s->x, i));
|
---|
| 573 | }
|
---|
| 574 | printf ("f() = %7.3f size = %.3f\n", s->fval, size);
|
---|
| 575 | }
|
---|
| 576 | while (status == GSL_CONTINUE && iter < 100);
|
---|
| 577 |
|
---|
| 578 | for (i=0;i<(size_t)np;i++)
|
---|
| 579 | gsl_vector_set(par->x, i, gsl_vector_get(s->x, i));
|
---|
| 580 | //gsl_vector_free(par->x);
|
---|
| 581 | gsl_vector_free(ss);
|
---|
| 582 | gsl_multimin_fminimizer_free (s);
|
---|
| 583 | };
|
---|