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#include <iostream> |
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< |
#include <cstdlib> |
3 |
< |
#include <cmath> |
2 |
> |
#include <stdlib.h> |
3 |
> |
#include <math.h> |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#include "simError.h" |
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|
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|
14 |
< |
template<typename T> Integrator<T>::Integrator( SimInfo *theInfo, ForceFields* the_ff ) { |
15 |
< |
|
14 |
> |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
15 |
> |
ForceFields* the_ff){ |
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info = theInfo; |
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myFF = the_ff; |
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isFirst = 1; |
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nMols = info->n_mol; |
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|
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// give a little love back to the SimInfo object |
24 |
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|
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if( info->the_integrator != NULL ) delete info->the_integrator; |
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info->the_integrator = this; |
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|
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if (info->the_integrator != NULL){ |
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delete info->the_integrator; |
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} |
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|
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nAtoms = info->n_atoms; |
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|
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// check for constraints |
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|
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constrainedA = NULL; |
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constrainedB = NULL; |
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|
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constrainedA = NULL; |
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constrainedB = NULL; |
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constrainedDsqr = NULL; |
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moving = NULL; |
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moved = NULL; |
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oldPos = NULL; |
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|
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moving = NULL; |
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moved = NULL; |
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oldPos = NULL; |
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|
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nConstrained = 0; |
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|
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checkConstraints(); |
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} |
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|
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template<typename T> Integrator<T>::~Integrator() { |
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|
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if( nConstrained ){ |
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template<typename T> Integrator<T>::~Integrator(){ |
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if (nConstrained){ |
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delete[] constrainedA; |
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delete[] constrainedB; |
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delete[] constrainedDsqr; |
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delete[] moved; |
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delete[] oldPos; |
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} |
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|
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} |
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|
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template<typename T> void Integrator<T>::checkConstraints( void ){ |
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|
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|
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template<typename T> void Integrator<T>::checkConstraints(void){ |
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isConstrained = 0; |
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|
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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Constraint* temp_con; |
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Constraint* dummy_plug; |
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temp_con = new Constraint[info->n_SRI]; |
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nConstrained = 0; |
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int constrained = 0; |
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|
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|
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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|
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theArray = (SRI**) molecules[i].getMyBonds(); |
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for(int j=0; j<molecules[i].getNBonds(); j++){ |
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|
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for (int i = 0; i < nMols; i++){ |
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theArray = (SRI * *) molecules[i].getMyBonds(); |
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for (int j = 0; j < molecules[i].getNBonds(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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|
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theArray = (SRI**) molecules[i].getMyBends(); |
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for(int j=0; j<molecules[i].getNBends(); j++){ |
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|
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theArray = (SRI * *) molecules[i].getMyBends(); |
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for (int j = 0; j < molecules[i].getNBends(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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nConstrained++; |
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constrained = 0; |
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|
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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|
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theArray = (SRI**) molecules[i].getMyTorsions(); |
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for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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|
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> |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
98 |
> |
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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|
101 |
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if(constrained){ |
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|
103 |
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dummy_plug = theArray[j]->get_constraint(); |
104 |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
105 |
< |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
108 |
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nConstrained++; |
118 |
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constrained = 0; |
100 |
> |
|
101 |
> |
if (constrained){ |
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> |
dummy_plug = theArray[j]->get_constraint(); |
103 |
> |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
104 |
> |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
105 |
> |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
106 |
> |
|
107 |
> |
nConstrained++; |
108 |
> |
constrained = 0; |
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} |
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} |
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} |
112 |
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|
113 |
< |
if(nConstrained > 0){ |
124 |
< |
|
113 |
> |
if (nConstrained > 0){ |
114 |
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isConstrained = 1; |
115 |
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|
116 |
< |
if(constrainedA != NULL ) delete[] constrainedA; |
117 |
< |
if(constrainedB != NULL ) delete[] constrainedB; |
118 |
< |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
116 |
> |
if (constrainedA != NULL) |
117 |
> |
delete[] constrainedA; |
118 |
> |
if (constrainedB != NULL) |
119 |
> |
delete[] constrainedB; |
120 |
> |
if (constrainedDsqr != NULL) |
121 |
> |
delete[] constrainedDsqr; |
122 |
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|
123 |
< |
constrainedA = new int[nConstrained]; |
124 |
< |
constrainedB = new int[nConstrained]; |
123 |
> |
constrainedA = new int[nConstrained]; |
124 |
> |
constrainedB = new int[nConstrained]; |
125 |
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constrainedDsqr = new double[nConstrained]; |
126 |
< |
|
127 |
< |
for( int i = 0; i < nConstrained; i++){ |
136 |
< |
|
126 |
> |
|
127 |
> |
for (int i = 0; i < nConstrained; i++){ |
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constrainedA[i] = temp_con[i].get_a(); |
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constrainedB[i] = temp_con[i].get_b(); |
130 |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
140 |
– |
|
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} |
132 |
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|
133 |
< |
|
133 |
> |
|
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// save oldAtoms to check for lode balanceing later on. |
135 |
< |
|
135 |
> |
|
136 |
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oldAtoms = nAtoms; |
137 |
< |
|
137 |
> |
|
138 |
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moving = new int[nAtoms]; |
139 |
< |
moved = new int[nAtoms]; |
139 |
> |
moved = new int[nAtoms]; |
140 |
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|
141 |
< |
oldPos = new double[nAtoms*3]; |
141 |
> |
oldPos = new double[nAtoms * 3]; |
142 |
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} |
143 |
< |
|
143 |
> |
|
144 |
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delete[] temp_con; |
145 |
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} |
146 |
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|
147 |
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|
148 |
< |
template<typename T> void Integrator<T>::integrate( void ){ |
148 |
> |
template<typename T> void Integrator<T>::integrate(void){ |
149 |
|
|
150 |
< |
int i, j; // loop counters |
151 |
< |
|
152 |
< |
double runTime = info->run_time; |
163 |
< |
double sampleTime = info->sampleTime; |
164 |
< |
double statusTime = info->statusTime; |
150 |
> |
double runTime = info->run_time; |
151 |
> |
double sampleTime = info->sampleTime; |
152 |
> |
double statusTime = info->statusTime; |
153 |
|
double thermalTime = info->thermalTime; |
154 |
+ |
double resetTime = info->resetTime; |
155 |
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|
156 |
+ |
|
157 |
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double currSample; |
158 |
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double currThermal; |
159 |
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double currStatus; |
160 |
+ |
double currReset; |
161 |
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|
162 |
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int calcPot, calcStress; |
172 |
– |
int isError; |
163 |
|
|
164 |
< |
tStats = new Thermo( info ); |
165 |
< |
statOut = new StatWriter( info ); |
166 |
< |
dumpOut = new DumpWriter( info ); |
164 |
> |
tStats = new Thermo(info); |
165 |
> |
statOut = new StatWriter(info); |
166 |
> |
dumpOut = new DumpWriter(info); |
167 |
|
|
168 |
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atoms = info->atoms; |
179 |
– |
DirectionalAtom* dAtom; |
169 |
|
|
170 |
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dt = info->dt; |
171 |
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dt2 = 0.5 * dt; |
172 |
|
|
173 |
+ |
readyCheck(); |
174 |
+ |
|
175 |
|
// initialize the forces before the first step |
176 |
|
|
177 |
+ |
std::cerr << "Before initial Force calc\n"; |
178 |
+ |
|
179 |
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calcForce(1, 1); |
180 |
< |
// myFF->doForces(1,1); |
181 |
< |
|
182 |
< |
if( info->setTemp ){ |
183 |
< |
|
180 |
> |
|
181 |
> |
if (nConstrained){ |
182 |
> |
preMove(); |
183 |
> |
constrainA(); |
184 |
> |
calcForce(1, 1); |
185 |
> |
constrainB(); |
186 |
> |
std::cerr << "premove done\n"; |
187 |
> |
} |
188 |
> |
|
189 |
> |
|
190 |
> |
|
191 |
> |
if (info->setTemp){ |
192 |
|
thermalize(); |
193 |
|
} |
194 |
< |
|
194 |
> |
|
195 |
|
calcPot = 0; |
196 |
|
calcStress = 0; |
197 |
< |
currSample = sampleTime; |
198 |
< |
currThermal = thermalTime; |
199 |
< |
currStatus = statusTime; |
197 |
> |
currSample = sampleTime + info->getTime(); |
198 |
> |
currThermal = thermalTime+ info->getTime(); |
199 |
> |
currStatus = statusTime + info->getTime(); |
200 |
> |
currReset = resetTime + info->getTime(); |
201 |
|
|
202 |
< |
dumpOut->writeDump( info->getTime() ); |
203 |
< |
statOut->writeStat( info->getTime() ); |
202 |
> |
dumpOut->writeDump(info->getTime()); |
203 |
> |
statOut->writeStat(info->getTime()); |
204 |
|
|
203 |
– |
readyCheck(); |
205 |
|
|
206 |
+ |
|
207 |
|
#ifdef IS_MPI |
208 |
< |
strcpy( checkPointMsg, |
207 |
< |
"The integrator is ready to go." ); |
208 |
> |
strcpy(checkPointMsg, "The integrator is ready to go."); |
209 |
|
MPIcheckPoint(); |
210 |
|
#endif // is_mpi |
211 |
|
|
212 |
< |
while( info->getTime() < runTime ){ |
213 |
< |
|
213 |
< |
if( (info->getTime()+dt) >= currStatus ){ |
212 |
> |
while (info->getTime() < runTime){ |
213 |
> |
if ((info->getTime() + dt) >= currStatus){ |
214 |
|
calcPot = 1; |
215 |
|
calcStress = 1; |
216 |
|
} |
217 |
|
|
218 |
< |
integrateStep( calcPot, calcStress ); |
219 |
< |
|
218 |
> |
integrateStep(calcPot, calcStress); |
219 |
> |
|
220 |
|
info->incrTime(dt); |
221 |
|
|
222 |
< |
if( info->setTemp ){ |
223 |
< |
if( info->getTime() >= currThermal ){ |
224 |
< |
thermalize(); |
225 |
< |
currThermal += thermalTime; |
222 |
> |
if (info->setTemp){ |
223 |
> |
if (info->getTime() >= currThermal){ |
224 |
> |
thermalize(); |
225 |
> |
currThermal += thermalTime; |
226 |
|
} |
227 |
|
} |
228 |
|
|
229 |
< |
if( info->getTime() >= currSample ){ |
230 |
< |
dumpOut->writeDump( info->getTime() ); |
229 |
> |
if (info->getTime() >= currSample){ |
230 |
> |
dumpOut->writeDump(info->getTime()); |
231 |
|
currSample += sampleTime; |
232 |
|
} |
233 |
|
|
234 |
< |
if( info->getTime() >= currStatus ){ |
235 |
< |
statOut->writeStat( info->getTime() ); |
236 |
< |
calcPot = 0; |
234 |
> |
if (info->getTime() >= currStatus){ |
235 |
> |
statOut->writeStat(info->getTime()); |
236 |
> |
calcPot = 0; |
237 |
|
calcStress = 0; |
238 |
|
currStatus += statusTime; |
239 |
< |
} |
239 |
> |
} |
240 |
|
|
241 |
+ |
if (info->resetIntegrator){ |
242 |
+ |
if (info->getTime() >= currReset){ |
243 |
+ |
this->resetIntegrator(); |
244 |
+ |
currReset += resetTime; |
245 |
+ |
} |
246 |
+ |
} |
247 |
+ |
|
248 |
+ |
std::cerr << "done with time = " << info->getTime() << "\n"; |
249 |
+ |
|
250 |
|
#ifdef IS_MPI |
251 |
< |
strcpy( checkPointMsg, |
243 |
< |
"successfully took a time step." ); |
251 |
> |
strcpy(checkPointMsg, "successfully took a time step."); |
252 |
|
MPIcheckPoint(); |
253 |
|
#endif // is_mpi |
246 |
– |
|
254 |
|
} |
255 |
|
|
249 |
– |
dumpOut->writeFinal(info->getTime()); |
256 |
|
|
257 |
+ |
// write the last frame |
258 |
+ |
dumpOut->writeDump(info->getTime()); |
259 |
+ |
|
260 |
|
delete dumpOut; |
261 |
|
delete statOut; |
262 |
|
} |
263 |
|
|
264 |
< |
template<typename T> void Integrator<T>::integrateStep( int calcPot, int calcStress ){ |
265 |
< |
|
257 |
< |
|
258 |
< |
|
264 |
> |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
265 |
> |
int calcStress){ |
266 |
|
// Position full step, and velocity half step |
260 |
– |
|
267 |
|
preMove(); |
268 |
+ |
|
269 |
|
moveA(); |
263 |
– |
if( nConstrained ) constrainA(); |
270 |
|
|
271 |
< |
|
271 |
> |
|
272 |
> |
|
273 |
> |
|
274 |
|
#ifdef IS_MPI |
275 |
< |
strcpy( checkPointMsg, "Succesful moveA\n" ); |
275 |
> |
strcpy(checkPointMsg, "Succesful moveA\n"); |
276 |
|
MPIcheckPoint(); |
277 |
|
#endif // is_mpi |
270 |
– |
|
278 |
|
|
279 |
+ |
|
280 |
|
// calc forces |
281 |
|
|
282 |
< |
calcForce(calcPot,calcStress); |
282 |
> |
calcForce(calcPot, calcStress); |
283 |
|
|
284 |
|
#ifdef IS_MPI |
285 |
< |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
285 |
> |
strcpy(checkPointMsg, "Succesful doForces\n"); |
286 |
|
MPIcheckPoint(); |
287 |
|
#endif // is_mpi |
280 |
– |
|
288 |
|
|
289 |
+ |
|
290 |
|
// finish the velocity half step |
291 |
< |
|
291 |
> |
|
292 |
|
moveB(); |
293 |
< |
if( nConstrained ) constrainB(); |
294 |
< |
|
293 |
> |
|
294 |
> |
|
295 |
> |
|
296 |
|
#ifdef IS_MPI |
297 |
< |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
297 |
> |
strcpy(checkPointMsg, "Succesful moveB\n"); |
298 |
|
MPIcheckPoint(); |
299 |
|
#endif // is_mpi |
291 |
– |
|
292 |
– |
|
300 |
|
} |
301 |
|
|
302 |
|
|
303 |
< |
template<typename T> void Integrator<T>::moveA( void ){ |
297 |
< |
|
303 |
> |
template<typename T> void Integrator<T>::moveA(void){ |
304 |
|
int i, j; |
305 |
|
DirectionalAtom* dAtom; |
306 |
|
double Tb[3], ji[3]; |
301 |
– |
double A[3][3], I[3][3]; |
302 |
– |
double angle; |
307 |
|
double vel[3], pos[3], frc[3]; |
308 |
|
double mass; |
309 |
|
|
310 |
< |
for( i=0; i<nAtoms; i++ ){ |
310 |
> |
for (i = 0; i < nAtoms; i++){ |
311 |
> |
atoms[i]->getVel(vel); |
312 |
> |
atoms[i]->getPos(pos); |
313 |
> |
atoms[i]->getFrc(frc); |
314 |
|
|
308 |
– |
atoms[i]->getVel( vel ); |
309 |
– |
atoms[i]->getPos( pos ); |
310 |
– |
atoms[i]->getFrc( frc ); |
311 |
– |
|
315 |
|
mass = atoms[i]->getMass(); |
316 |
|
|
317 |
< |
for (j=0; j < 3; j++) { |
317 |
> |
for (j = 0; j < 3; j++){ |
318 |
|
// velocity half step |
319 |
< |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
319 |
> |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
320 |
|
// position whole step |
321 |
|
pos[j] += dt * vel[j]; |
322 |
|
} |
323 |
|
|
324 |
< |
atoms[i]->setVel( vel ); |
325 |
< |
atoms[i]->setPos( pos ); |
324 |
> |
atoms[i]->setVel(vel); |
325 |
> |
atoms[i]->setPos(pos); |
326 |
|
|
327 |
< |
if( atoms[i]->isDirectional() ){ |
327 |
> |
if (atoms[i]->isDirectional()){ |
328 |
> |
dAtom = (DirectionalAtom *) atoms[i]; |
329 |
|
|
326 |
– |
dAtom = (DirectionalAtom *)atoms[i]; |
327 |
– |
|
330 |
|
// get and convert the torque to body frame |
329 |
– |
|
330 |
– |
dAtom->getTrq( Tb ); |
331 |
– |
dAtom->lab2Body( Tb ); |
331 |
|
|
332 |
+ |
dAtom->getTrq(Tb); |
333 |
+ |
dAtom->lab2Body(Tb); |
334 |
+ |
|
335 |
|
// get the angular momentum, and propagate a half step |
336 |
|
|
337 |
< |
dAtom->getJ( ji ); |
337 |
> |
dAtom->getJ(ji); |
338 |
|
|
339 |
< |
for (j=0; j < 3; j++) |
339 |
> |
for (j = 0; j < 3; j++) |
340 |
|
ji[j] += (dt2 * Tb[j]) * eConvert; |
339 |
– |
|
340 |
– |
// use the angular velocities to propagate the rotation matrix a |
341 |
– |
// full time step |
341 |
|
|
342 |
< |
dAtom->getA(A); |
344 |
< |
dAtom->getI(I); |
345 |
< |
|
346 |
< |
// rotate about the x-axis |
347 |
< |
angle = dt2 * ji[0] / I[0][0]; |
348 |
< |
this->rotate( 1, 2, angle, ji, A ); |
342 |
> |
this->rotationPropagation( dAtom, ji ); |
343 |
|
|
344 |
< |
// rotate about the y-axis |
345 |
< |
angle = dt2 * ji[1] / I[1][1]; |
346 |
< |
this->rotate( 2, 0, angle, ji, A ); |
353 |
< |
|
354 |
< |
// rotate about the z-axis |
355 |
< |
angle = dt * ji[2] / I[2][2]; |
356 |
< |
this->rotate( 0, 1, angle, ji, A); |
357 |
< |
|
358 |
< |
// rotate about the y-axis |
359 |
< |
angle = dt2 * ji[1] / I[1][1]; |
360 |
< |
this->rotate( 2, 0, angle, ji, A ); |
361 |
< |
|
362 |
< |
// rotate about the x-axis |
363 |
< |
angle = dt2 * ji[0] / I[0][0]; |
364 |
< |
this->rotate( 1, 2, angle, ji, A ); |
365 |
< |
|
344 |
> |
dAtom->setJ(ji); |
345 |
> |
} |
346 |
> |
} |
347 |
|
|
348 |
< |
dAtom->setJ( ji ); |
349 |
< |
dAtom->setA( A ); |
369 |
< |
|
370 |
< |
} |
348 |
> |
if (nConstrained){ |
349 |
> |
constrainA(); |
350 |
|
} |
351 |
|
} |
352 |
|
|
353 |
|
|
354 |
< |
template<typename T> void Integrator<T>::moveB( void ){ |
354 |
> |
template<typename T> void Integrator<T>::moveB(void){ |
355 |
|
int i, j; |
356 |
|
DirectionalAtom* dAtom; |
357 |
|
double Tb[3], ji[3]; |
358 |
|
double vel[3], frc[3]; |
359 |
|
double mass; |
360 |
|
|
361 |
< |
for( i=0; i<nAtoms; i++ ){ |
362 |
< |
|
363 |
< |
atoms[i]->getVel( vel ); |
385 |
< |
atoms[i]->getFrc( frc ); |
361 |
> |
for (i = 0; i < nAtoms; i++){ |
362 |
> |
atoms[i]->getVel(vel); |
363 |
> |
atoms[i]->getFrc(frc); |
364 |
|
|
365 |
|
mass = atoms[i]->getMass(); |
366 |
|
|
367 |
|
// velocity half step |
368 |
< |
for (j=0; j < 3; j++) |
369 |
< |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
392 |
< |
|
393 |
< |
atoms[i]->setVel( vel ); |
394 |
< |
|
395 |
< |
if( atoms[i]->isDirectional() ){ |
368 |
> |
for (j = 0; j < 3; j++) |
369 |
> |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
370 |
|
|
371 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
371 |
> |
atoms[i]->setVel(vel); |
372 |
|
|
373 |
< |
// get and convert the torque to body frame |
373 |
> |
if (atoms[i]->isDirectional()){ |
374 |
> |
dAtom = (DirectionalAtom *) atoms[i]; |
375 |
|
|
376 |
< |
dAtom->getTrq( Tb ); |
402 |
< |
dAtom->lab2Body( Tb ); |
376 |
> |
// get and convert the torque to body frame |
377 |
|
|
378 |
+ |
dAtom->getTrq(Tb); |
379 |
+ |
dAtom->lab2Body(Tb); |
380 |
+ |
|
381 |
|
// get the angular momentum, and propagate a half step |
382 |
|
|
383 |
< |
dAtom->getJ( ji ); |
383 |
> |
dAtom->getJ(ji); |
384 |
|
|
385 |
< |
for (j=0; j < 3; j++) |
385 |
> |
for (j = 0; j < 3; j++) |
386 |
|
ji[j] += (dt2 * Tb[j]) * eConvert; |
410 |
– |
|
387 |
|
|
388 |
< |
dAtom->setJ( ji ); |
388 |
> |
|
389 |
> |
dAtom->setJ(ji); |
390 |
|
} |
391 |
|
} |
392 |
+ |
|
393 |
+ |
if (nConstrained){ |
394 |
+ |
constrainB(); |
395 |
+ |
} |
396 |
|
} |
397 |
|
|
398 |
< |
template<typename T> void Integrator<T>::preMove( void ){ |
398 |
> |
template<typename T> void Integrator<T>::preMove(void){ |
399 |
|
int i, j; |
400 |
|
double pos[3]; |
401 |
|
|
402 |
< |
if( nConstrained ){ |
402 |
> |
if (nConstrained){ |
403 |
> |
for (i = 0; i < nAtoms; i++){ |
404 |
> |
atoms[i]->getPos(pos); |
405 |
|
|
406 |
< |
for(i=0; i < nAtoms; i++) { |
407 |
< |
|
425 |
< |
atoms[i]->getPos( pos ); |
426 |
< |
|
427 |
< |
for (j = 0; j < 3; j++) { |
428 |
< |
oldPos[3*i + j] = pos[j]; |
406 |
> |
for (j = 0; j < 3; j++){ |
407 |
> |
oldPos[3 * i + j] = pos[j]; |
408 |
|
} |
430 |
– |
|
409 |
|
} |
410 |
< |
} |
410 |
> |
} |
411 |
|
} |
412 |
|
|
413 |
|
template<typename T> void Integrator<T>::constrainA(){ |
414 |
< |
|
437 |
< |
int i,j,k; |
414 |
> |
int i, j; |
415 |
|
int done; |
416 |
|
double posA[3], posB[3]; |
417 |
|
double velA[3], velB[3]; |
426 |
|
double gab; |
427 |
|
int iteration; |
428 |
|
|
429 |
< |
for( i=0; i<nAtoms; i++){ |
429 |
> |
for (i = 0; i < nAtoms; i++){ |
430 |
|
moving[i] = 0; |
431 |
< |
moved[i] = 1; |
431 |
> |
moved[i] = 1; |
432 |
|
} |
433 |
|
|
434 |
|
iteration = 0; |
435 |
|
done = 0; |
436 |
< |
while( !done && (iteration < maxIteration )){ |
460 |
< |
|
436 |
> |
while (!done && (iteration < maxIteration)){ |
437 |
|
done = 1; |
438 |
< |
for(i=0; i<nConstrained; i++){ |
463 |
< |
|
438 |
> |
for (i = 0; i < nConstrained; i++){ |
439 |
|
a = constrainedA[i]; |
440 |
|
b = constrainedB[i]; |
466 |
– |
|
467 |
– |
ax = (a*3) + 0; |
468 |
– |
ay = (a*3) + 1; |
469 |
– |
az = (a*3) + 2; |
441 |
|
|
442 |
< |
bx = (b*3) + 0; |
443 |
< |
by = (b*3) + 1; |
444 |
< |
bz = (b*3) + 2; |
442 |
> |
ax = (a * 3) + 0; |
443 |
> |
ay = (a * 3) + 1; |
444 |
> |
az = (a * 3) + 2; |
445 |
|
|
446 |
< |
if( moved[a] || moved[b] ){ |
447 |
< |
|
448 |
< |
atoms[a]->getPos( posA ); |
449 |
< |
atoms[b]->getPos( posB ); |
450 |
< |
|
451 |
< |
for (j = 0; j < 3; j++ ) |
446 |
> |
bx = (b * 3) + 0; |
447 |
> |
by = (b * 3) + 1; |
448 |
> |
bz = (b * 3) + 2; |
449 |
> |
|
450 |
> |
if (moved[a] || moved[b]){ |
451 |
> |
atoms[a]->getPos(posA); |
452 |
> |
atoms[b]->getPos(posB); |
453 |
> |
|
454 |
> |
for (j = 0; j < 3; j++) |
455 |
|
pab[j] = posA[j] - posB[j]; |
482 |
– |
|
483 |
– |
//periodic boundary condition |
456 |
|
|
457 |
< |
info->wrapVector( pab ); |
457 |
> |
//periodic boundary condition |
458 |
|
|
459 |
< |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
459 |
> |
info->wrapVector(pab); |
460 |
|
|
461 |
< |
rabsq = constrainedDsqr[i]; |
490 |
< |
diffsq = rabsq - pabsq; |
461 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
462 |
|
|
463 |
< |
// the original rattle code from alan tidesley |
464 |
< |
if (fabs(diffsq) > (tol*rabsq*2)) { |
494 |
< |
rab[0] = oldPos[ax] - oldPos[bx]; |
495 |
< |
rab[1] = oldPos[ay] - oldPos[by]; |
496 |
< |
rab[2] = oldPos[az] - oldPos[bz]; |
463 |
> |
rabsq = constrainedDsqr[i]; |
464 |
> |
diffsq = rabsq - pabsq; |
465 |
|
|
466 |
< |
info->wrapVector( rab ); |
466 |
> |
// the original rattle code from alan tidesley |
467 |
> |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
468 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
469 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
470 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
471 |
|
|
472 |
< |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
472 |
> |
info->wrapVector(rab); |
473 |
|
|
474 |
< |
rpabsq = rpab * rpab; |
474 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
475 |
|
|
476 |
+ |
rpabsq = rpab * rpab; |
477 |
|
|
505 |
– |
if (rpabsq < (rabsq * -diffsq)){ |
478 |
|
|
479 |
+ |
if (rpabsq < (rabsq * -diffsq)){ |
480 |
|
#ifdef IS_MPI |
481 |
< |
a = atoms[a]->getGlobalIndex(); |
482 |
< |
b = atoms[b]->getGlobalIndex(); |
481 |
> |
a = atoms[a]->getGlobalIndex(); |
482 |
> |
b = atoms[b]->getGlobalIndex(); |
483 |
|
#endif //is_mpi |
484 |
< |
sprintf( painCave.errMsg, |
485 |
< |
"Constraint failure in constrainA at atom %d and %d.\n", |
486 |
< |
a, b ); |
487 |
< |
painCave.isFatal = 1; |
488 |
< |
simError(); |
489 |
< |
} |
484 |
> |
sprintf(painCave.errMsg, |
485 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
486 |
> |
b); |
487 |
> |
painCave.isFatal = 1; |
488 |
> |
simError(); |
489 |
> |
} |
490 |
|
|
491 |
< |
rma = 1.0 / atoms[a]->getMass(); |
492 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
491 |
> |
rma = 1.0 / atoms[a]->getMass(); |
492 |
> |
rmb = 1.0 / atoms[b]->getMass(); |
493 |
|
|
494 |
< |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
494 |
> |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
495 |
|
|
496 |
|
dx = rab[0] * gab; |
497 |
|
dy = rab[1] * gab; |
498 |
|
dz = rab[2] * gab; |
499 |
|
|
500 |
< |
posA[0] += rma * dx; |
501 |
< |
posA[1] += rma * dy; |
502 |
< |
posA[2] += rma * dz; |
500 |
> |
posA[0] += rma * dx; |
501 |
> |
posA[1] += rma * dy; |
502 |
> |
posA[2] += rma * dz; |
503 |
|
|
504 |
< |
atoms[a]->setPos( posA ); |
504 |
> |
atoms[a]->setPos(posA); |
505 |
|
|
506 |
< |
posB[0] -= rmb * dx; |
507 |
< |
posB[1] -= rmb * dy; |
508 |
< |
posB[2] -= rmb * dz; |
506 |
> |
posB[0] -= rmb * dx; |
507 |
> |
posB[1] -= rmb * dy; |
508 |
> |
posB[2] -= rmb * dz; |
509 |
|
|
510 |
< |
atoms[b]->setPos( posB ); |
510 |
> |
atoms[b]->setPos(posB); |
511 |
|
|
512 |
|
dx = dx / dt; |
513 |
|
dy = dy / dt; |
514 |
|
dz = dz / dt; |
515 |
|
|
516 |
< |
atoms[a]->getVel( velA ); |
516 |
> |
atoms[a]->getVel(velA); |
517 |
|
|
518 |
< |
velA[0] += rma * dx; |
519 |
< |
velA[1] += rma * dy; |
520 |
< |
velA[2] += rma * dz; |
518 |
> |
velA[0] += rma * dx; |
519 |
> |
velA[1] += rma * dy; |
520 |
> |
velA[2] += rma * dz; |
521 |
|
|
522 |
< |
atoms[a]->setVel( velA ); |
522 |
> |
atoms[a]->setVel(velA); |
523 |
|
|
524 |
< |
atoms[b]->getVel( velB ); |
524 |
> |
atoms[b]->getVel(velB); |
525 |
|
|
526 |
< |
velB[0] -= rmb * dx; |
527 |
< |
velB[1] -= rmb * dy; |
528 |
< |
velB[2] -= rmb * dz; |
526 |
> |
velB[0] -= rmb * dx; |
527 |
> |
velB[1] -= rmb * dy; |
528 |
> |
velB[2] -= rmb * dz; |
529 |
|
|
530 |
< |
atoms[b]->setVel( velB ); |
530 |
> |
atoms[b]->setVel(velB); |
531 |
|
|
532 |
< |
moving[a] = 1; |
533 |
< |
moving[b] = 1; |
534 |
< |
done = 0; |
535 |
< |
} |
532 |
> |
moving[a] = 1; |
533 |
> |
moving[b] = 1; |
534 |
> |
done = 0; |
535 |
> |
} |
536 |
|
} |
537 |
|
} |
538 |
< |
|
539 |
< |
for(i=0; i<nAtoms; i++){ |
567 |
< |
|
538 |
> |
|
539 |
> |
for (i = 0; i < nAtoms; i++){ |
540 |
|
moved[i] = moving[i]; |
541 |
|
moving[i] = 0; |
542 |
|
} |
544 |
|
iteration++; |
545 |
|
} |
546 |
|
|
547 |
< |
if( !done ){ |
548 |
< |
|
549 |
< |
sprintf( painCave.errMsg, |
550 |
< |
"Constraint failure in constrainA, too many iterations: %d\n", |
579 |
< |
iteration ); |
547 |
> |
if (!done){ |
548 |
> |
sprintf(painCave.errMsg, |
549 |
> |
"Constraint failure in constrainA, too many iterations: %d\n", |
550 |
> |
iteration); |
551 |
|
painCave.isFatal = 1; |
552 |
|
simError(); |
553 |
|
} |
554 |
|
|
555 |
|
} |
556 |
|
|
557 |
< |
template<typename T> void Integrator<T>::constrainB( void ){ |
558 |
< |
|
588 |
< |
int i,j,k; |
557 |
> |
template<typename T> void Integrator<T>::constrainB(void){ |
558 |
> |
int i, j; |
559 |
|
int done; |
560 |
|
double posA[3], posB[3]; |
561 |
|
double velA[3], velB[3]; |
564 |
|
int a, b, ax, ay, az, bx, by, bz; |
565 |
|
double rma, rmb; |
566 |
|
double dx, dy, dz; |
567 |
< |
double rabsq, pabsq, rvab; |
598 |
< |
double diffsq; |
567 |
> |
double rvab; |
568 |
|
double gab; |
569 |
|
int iteration; |
570 |
|
|
571 |
< |
for(i=0; i<nAtoms; i++){ |
571 |
> |
for (i = 0; i < nAtoms; i++){ |
572 |
|
moving[i] = 0; |
573 |
|
moved[i] = 1; |
574 |
|
} |
575 |
|
|
576 |
|
done = 0; |
577 |
|
iteration = 0; |
578 |
< |
while( !done && (iteration < maxIteration ) ){ |
610 |
< |
|
578 |
> |
while (!done && (iteration < maxIteration)){ |
579 |
|
done = 1; |
580 |
|
|
581 |
< |
for(i=0; i<nConstrained; i++){ |
614 |
< |
|
581 |
> |
for (i = 0; i < nConstrained; i++){ |
582 |
|
a = constrainedA[i]; |
583 |
|
b = constrainedB[i]; |
584 |
|
|
585 |
< |
ax = (a*3) + 0; |
586 |
< |
ay = (a*3) + 1; |
587 |
< |
az = (a*3) + 2; |
585 |
> |
ax = (a * 3) + 0; |
586 |
> |
ay = (a * 3) + 1; |
587 |
> |
az = (a * 3) + 2; |
588 |
|
|
589 |
< |
bx = (b*3) + 0; |
590 |
< |
by = (b*3) + 1; |
591 |
< |
bz = (b*3) + 2; |
589 |
> |
bx = (b * 3) + 0; |
590 |
> |
by = (b * 3) + 1; |
591 |
> |
bz = (b * 3) + 2; |
592 |
|
|
593 |
< |
if( moved[a] || moved[b] ){ |
593 |
> |
if (moved[a] || moved[b]){ |
594 |
> |
atoms[a]->getVel(velA); |
595 |
> |
atoms[b]->getVel(velB); |
596 |
|
|
597 |
< |
atoms[a]->getVel( velA ); |
598 |
< |
atoms[b]->getVel( velB ); |
599 |
< |
|
631 |
< |
vxab = velA[0] - velB[0]; |
632 |
< |
vyab = velA[1] - velB[1]; |
633 |
< |
vzab = velA[2] - velB[2]; |
597 |
> |
vxab = velA[0] - velB[0]; |
598 |
> |
vyab = velA[1] - velB[1]; |
599 |
> |
vzab = velA[2] - velB[2]; |
600 |
|
|
601 |
< |
atoms[a]->getPos( posA ); |
602 |
< |
atoms[b]->getPos( posB ); |
601 |
> |
atoms[a]->getPos(posA); |
602 |
> |
atoms[b]->getPos(posB); |
603 |
|
|
604 |
< |
for (j = 0; j < 3; j++) |
604 |
> |
for (j = 0; j < 3; j++) |
605 |
|
rab[j] = posA[j] - posB[j]; |
640 |
– |
|
641 |
– |
info->wrapVector( rab ); |
642 |
– |
|
643 |
– |
rma = 1.0 / atoms[a]->getMass(); |
644 |
– |
rmb = 1.0 / atoms[b]->getMass(); |
606 |
|
|
607 |
< |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
647 |
< |
|
648 |
< |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
607 |
> |
info->wrapVector(rab); |
608 |
|
|
609 |
< |
if (fabs(gab) > tol) { |
610 |
< |
|
652 |
< |
dx = rab[0] * gab; |
653 |
< |
dy = rab[1] * gab; |
654 |
< |
dz = rab[2] * gab; |
655 |
< |
|
656 |
< |
velA[0] += rma * dx; |
657 |
< |
velA[1] += rma * dy; |
658 |
< |
velA[2] += rma * dz; |
609 |
> |
rma = 1.0 / atoms[a]->getMass(); |
610 |
> |
rmb = 1.0 / atoms[b]->getMass(); |
611 |
|
|
612 |
< |
atoms[a]->setVel( velA ); |
612 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
613 |
|
|
614 |
< |
velB[0] -= rmb * dx; |
663 |
< |
velB[1] -= rmb * dy; |
664 |
< |
velB[2] -= rmb * dz; |
614 |
> |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
615 |
|
|
616 |
< |
atoms[b]->setVel( velB ); |
617 |
< |
|
618 |
< |
moving[a] = 1; |
619 |
< |
moving[b] = 1; |
620 |
< |
done = 0; |
621 |
< |
} |
616 |
> |
if (fabs(gab) > tol){ |
617 |
> |
dx = rab[0] * gab; |
618 |
> |
dy = rab[1] * gab; |
619 |
> |
dz = rab[2] * gab; |
620 |
> |
|
621 |
> |
velA[0] += rma * dx; |
622 |
> |
velA[1] += rma * dy; |
623 |
> |
velA[2] += rma * dz; |
624 |
> |
|
625 |
> |
atoms[a]->setVel(velA); |
626 |
> |
|
627 |
> |
velB[0] -= rmb * dx; |
628 |
> |
velB[1] -= rmb * dy; |
629 |
> |
velB[2] -= rmb * dz; |
630 |
> |
|
631 |
> |
atoms[b]->setVel(velB); |
632 |
> |
|
633 |
> |
moving[a] = 1; |
634 |
> |
moving[b] = 1; |
635 |
> |
done = 0; |
636 |
> |
} |
637 |
|
} |
638 |
|
} |
639 |
|
|
640 |
< |
for(i=0; i<nAtoms; i++){ |
640 |
> |
for (i = 0; i < nAtoms; i++){ |
641 |
|
moved[i] = moving[i]; |
642 |
|
moving[i] = 0; |
643 |
|
} |
644 |
< |
|
644 |
> |
|
645 |
|
iteration++; |
646 |
|
} |
682 |
– |
|
683 |
– |
if( !done ){ |
647 |
|
|
648 |
< |
|
649 |
< |
sprintf( painCave.errMsg, |
650 |
< |
"Constraint failure in constrainB, too many iterations: %d\n", |
651 |
< |
iteration ); |
648 |
> |
if (!done){ |
649 |
> |
sprintf(painCave.errMsg, |
650 |
> |
"Constraint failure in constrainB, too many iterations: %d\n", |
651 |
> |
iteration); |
652 |
|
painCave.isFatal = 1; |
653 |
|
simError(); |
654 |
< |
} |
692 |
< |
|
654 |
> |
} |
655 |
|
} |
656 |
|
|
657 |
< |
template<typename T> void Integrator<T>::rotate( int axes1, int axes2, double angle, double ji[3], |
658 |
< |
double A[3][3] ){ |
657 |
> |
template<typename T> void Integrator<T>::rotationPropagation |
658 |
> |
( DirectionalAtom* dAtom, double ji[3] ){ |
659 |
|
|
660 |
< |
int i,j,k; |
660 |
> |
double angle; |
661 |
> |
double A[3][3], I[3][3]; |
662 |
> |
|
663 |
> |
// use the angular velocities to propagate the rotation matrix a |
664 |
> |
// full time step |
665 |
> |
|
666 |
> |
dAtom->getA(A); |
667 |
> |
dAtom->getI(I); |
668 |
> |
|
669 |
> |
// rotate about the x-axis |
670 |
> |
angle = dt2 * ji[0] / I[0][0]; |
671 |
> |
this->rotate( 1, 2, angle, ji, A ); |
672 |
> |
|
673 |
> |
// rotate about the y-axis |
674 |
> |
angle = dt2 * ji[1] / I[1][1]; |
675 |
> |
this->rotate( 2, 0, angle, ji, A ); |
676 |
> |
|
677 |
> |
// rotate about the z-axis |
678 |
> |
angle = dt * ji[2] / I[2][2]; |
679 |
> |
this->rotate( 0, 1, angle, ji, A); |
680 |
> |
|
681 |
> |
// rotate about the y-axis |
682 |
> |
angle = dt2 * ji[1] / I[1][1]; |
683 |
> |
this->rotate( 2, 0, angle, ji, A ); |
684 |
> |
|
685 |
> |
// rotate about the x-axis |
686 |
> |
angle = dt2 * ji[0] / I[0][0]; |
687 |
> |
this->rotate( 1, 2, angle, ji, A ); |
688 |
> |
|
689 |
> |
dAtom->setA( A ); |
690 |
> |
} |
691 |
> |
|
692 |
> |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
693 |
> |
double angle, double ji[3], |
694 |
> |
double A[3][3]){ |
695 |
> |
int i, j, k; |
696 |
|
double sinAngle; |
697 |
|
double cosAngle; |
698 |
|
double angleSqr; |
704 |
|
|
705 |
|
// initialize the tempA |
706 |
|
|
707 |
< |
for(i=0; i<3; i++){ |
708 |
< |
for(j=0; j<3; j++){ |
707 |
> |
for (i = 0; i < 3; i++){ |
708 |
> |
for (j = 0; j < 3; j++){ |
709 |
|
tempA[j][i] = A[i][j]; |
710 |
|
} |
711 |
|
} |
712 |
|
|
713 |
|
// initialize the tempJ |
714 |
|
|
715 |
< |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
716 |
< |
|
715 |
> |
for (i = 0; i < 3; i++) |
716 |
> |
tempJ[i] = ji[i]; |
717 |
> |
|
718 |
|
// initalize rot as a unit matrix |
719 |
|
|
720 |
|
rot[0][0] = 1.0; |
724 |
|
rot[1][0] = 0.0; |
725 |
|
rot[1][1] = 1.0; |
726 |
|
rot[1][2] = 0.0; |
727 |
< |
|
727 |
> |
|
728 |
|
rot[2][0] = 0.0; |
729 |
|
rot[2][1] = 0.0; |
730 |
|
rot[2][2] = 1.0; |
731 |
< |
|
731 |
> |
|
732 |
|
// use a small angle aproximation for sin and cosine |
733 |
|
|
734 |
< |
angleSqr = angle * angle; |
734 |
> |
angleSqr = angle * angle; |
735 |
|
angleSqrOver4 = angleSqr / 4.0; |
736 |
|
top = 1.0 - angleSqrOver4; |
737 |
|
bottom = 1.0 + angleSqrOver4; |
744 |
|
|
745 |
|
rot[axes1][axes2] = sinAngle; |
746 |
|
rot[axes2][axes1] = -sinAngle; |
747 |
< |
|
747 |
> |
|
748 |
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
749 |
< |
|
750 |
< |
for(i=0; i<3; i++){ |
749 |
> |
|
750 |
> |
for (i = 0; i < 3; i++){ |
751 |
|
ji[i] = 0.0; |
752 |
< |
for(k=0; k<3; k++){ |
752 |
> |
for (k = 0; k < 3; k++){ |
753 |
|
ji[i] += rot[i][k] * tempJ[k]; |
754 |
|
} |
755 |
|
} |
756 |
|
|
757 |
< |
// rotate the Rotation matrix acording to: |
757 |
> |
// rotate the Rotation matrix acording to: |
758 |
|
// A[][] = A[][] * transpose(rot[][]) |
759 |
|
|
760 |
|
|
762 |
|
// calculation as: |
763 |
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
764 |
|
|
765 |
< |
for(i=0; i<3; i++){ |
766 |
< |
for(j=0; j<3; j++){ |
765 |
> |
for (i = 0; i < 3; i++){ |
766 |
> |
for (j = 0; j < 3; j++){ |
767 |
|
A[j][i] = 0.0; |
768 |
< |
for(k=0; k<3; k++){ |
769 |
< |
A[j][i] += tempA[i][k] * rot[j][k]; |
768 |
> |
for (k = 0; k < 3; k++){ |
769 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
770 |
|
} |
771 |
|
} |
772 |
|
} |
773 |
|
} |
774 |
|
|
775 |
< |
template<typename T> void Integrator<T>::calcForce( int calcPot, int calcStress ){ |
776 |
< |
myFF->doForces(calcPot,calcStress); |
779 |
< |
|
775 |
> |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
776 |
> |
myFF->doForces(calcPot, calcStress); |
777 |
|
} |
778 |
|
|
779 |
|
template<typename T> void Integrator<T>::thermalize(){ |
780 |
< |
tStats->velocitize(); |
780 |
> |
tStats->velocitize(); |
781 |
|
} |
782 |
+ |
|
783 |
+ |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
784 |
+ |
return tStats->getTotalE(); |
785 |
+ |
} |
786 |
+ |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
787 |
+ |
//By default, return a null string |
788 |
+ |
//The reason we use string instead of char* is that if we use char*, we will |
789 |
+ |
//return a pointer point to local variable which might cause problem |
790 |
+ |
return string(); |
791 |
+ |
} |