ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/NPTi.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 600 by gezelter, Mon Jul 14 22:38:13 2003 UTC vs.
Revision 857 by mmeineke, Fri Nov 7 17:09:48 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2   #include "Atom.hpp"
3   #include "SRI.hpp"
4   #include "AbstractClasses.hpp"
# Line 7 | Line 7
7   #include "Thermo.hpp"
8   #include "ReadWrite.hpp"
9   #include "Integrator.hpp"
10 < #include "simError.h"
10 > #include "simError.h"
11  
12 + #ifdef IS_MPI
13 + #include "mpiSimulation.hpp"
14 + #endif
15  
16   // Basic isotropic thermostating and barostating via the Melchionna
17   // modification of the Hoover algorithm:
18   //
19   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
20 < //       Molec. Phys., 78, 533.
20 > //       Molec. Phys., 78, 533.
21   //
22   //           and
23 < //
23 > //
24   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25  
26 < NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 <  Integrator( theInfo, the_ff )
26 > template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 >  T( theInfo, the_ff )
28   {
29 <  chi = 0.0;
29 >  GenericData* data;
30 >  DoubleArrayData * etaValue;
31 >  vector<double> etaArray;
32 >
33    eta = 0.0;
34 <  have_tau_thermostat = 0;
35 <  have_tau_barostat = 0;
36 <  have_target_temp = 0;
37 <  have_target_pressure = 0;
34 >  oldEta = 0.0;
35 >
36 >  if( theInfo->useInitXSstate ){
37 >    // retrieve eta from simInfo if
38 >    data = info->getProperty(ETAVALUE_ID);
39 >    if(data){
40 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
41 >      
42 >      if(etaValue){
43 >        etaArray = etaValue->getData();
44 >        eta = etaArray[0];
45 >        oldEta = eta;
46 >      }
47 >    }
48 >  }
49   }
50  
51 < void NPTi::moveA() {
52 <  
53 <  int i, j;
37 <  DirectionalAtom* dAtom;
38 <  double Tb[3], ji[3];
39 <  double A[3][3], I[3][3];
40 <  double angle, mass;
41 <  double vel[3], pos[3], frc[3];
51 > template<typename T> NPTi<T>::~NPTi() {
52 >  //nothing for now
53 > }
54  
55 <  double rj[3];
56 <  double instaTemp, instaPress, instaVol;
57 <  double tt2, tb2;
55 > template<typename T> void NPTi<T>::resetIntegrator() {
56 >  eta = 0.0;
57 >  T::resetIntegrator();
58 > }
59  
60 <  tt2 = tauThermostat * tauThermostat;
61 <  tb2 = tauBarostat * tauBarostat;
49 <
50 <  instaTemp = tStats->getTemperature();
51 <  instaPress = tStats->getPressure();
52 <  instaVol = tStats->getVolume();
53 <  
54 <   // first evolve chi a half step
55 <  
56 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
57 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
60 > template<typename T> void NPTi<T>::evolveEtaA() {
61 >  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
62                   (p_convert*NkBT*tb2));
63 +  oldEta = eta;
64 + }
65  
66 <  for( i=0; i<nAtoms; i++ ){
61 <    atoms[i]->getVel( vel );
62 <    atoms[i]->getPos( pos );
63 <    atoms[i]->getFrc( frc );
66 > template<typename T> void NPTi<T>::evolveEtaB() {
67  
68 <    mass = atoms[i]->getMass();
68 >  prevEta = eta;
69 >  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
70 >                 (p_convert*NkBT*tb2));
71 > }
72  
73 <    for (j=0; j < 3; j++) {
74 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
75 <      rj[j] = pos[j];
70 <    }
73 > template<typename T> void NPTi<T>::calcVelScale(void) {
74 >  vScale = chi + eta;
75 > }
76  
77 <    atoms[i]->setVel( vel );
77 > template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
78 >  int i;
79  
80 <    info->wrapVector(rj);
80 >  for(i=0; i<3; i++) sc[i] = vel[i] * vScale;
81 > }
82  
83 <    for (j = 0; j < 3; j++)
84 <      pos[j] += dt * (vel[j] + eta*rj[j]);
83 > template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
84 >  int i;
85  
86 +  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale;
87 + }
88  
80 –    atoms[i]->setPos( pos );
89  
90 + template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
91 +                                               int index, double sc[3]){
92 +  int j;
93  
94 <    if( atoms[i]->isDirectional() ){
94 >  for(j=0; j<3; j++)
95 >    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
96  
97 <      dAtom = (DirectionalAtom *)atoms[i];
98 <          
99 <      // get and convert the torque to body frame
88 <      
89 <      dAtom->getTrq( Tb );
90 <      dAtom->lab2Body( Tb );
91 <      
92 <      // get the angular momentum, and propagate a half step
97 >  for(j=0; j<3; j++)
98 >    sc[j] *= eta;
99 > }
100  
101 <      dAtom->getJ( ji );
101 > template<typename T> void NPTi<T>::scaleSimBox( void ){
102  
103 <      for (j=0; j < 3; j++)
97 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
98 <      
99 <      // use the angular velocities to propagate the rotation matrix a
100 <      // full time step
103 >  double scaleFactor;
104  
105 <      dAtom->getA(A);
103 <      dAtom->getI(I);
104 <    
105 <      // rotate about the x-axis      
106 <      angle = dt2 * ji[0] / I[0][0];
107 <      this->rotate( 1, 2, angle, ji, A );
105 >  scaleFactor = exp(dt*eta);
106  
107 <      // rotate about the y-axis
108 <      angle = dt2 * ji[1] / I[1][1];
109 <      this->rotate( 2, 0, angle, ji, A );
110 <      
111 <      // rotate about the z-axis
112 <      angle = dt * ji[2] / I[2][2];
113 <      this->rotate( 0, 1, angle, ji, A);
114 <      
115 <      // rotate about the y-axis
116 <      angle = dt2 * ji[1] / I[1][1];
119 <      this->rotate( 2, 0, angle, ji, A );
120 <      
121 <       // rotate about the x-axis
122 <      angle = dt2 * ji[0] / I[0][0];
123 <      this->rotate( 1, 2, angle, ji, A );
124 <      
125 <      dAtom->setJ( ji );
126 <      dAtom->setA( A  );    
127 <    }                
128 <
107 >  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
108 >    sprintf( painCave.errMsg,
109 >             "NPTi error: Attempting a Box scaling of more than 10 percent"
110 >             " check your tauBarostat, as it is probably too small!\n"
111 >             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
112 >             );
113 >    painCave.isFatal = 1;
114 >    simError();
115 >  } else {
116 >    info->scaleBox(scaleFactor);
117    }
118 <  // Scale the box after all the positions have been moved:
131 <  
132 <  cerr << "eta = " << eta
133 <       << "; exp(dt*eta) = " << exp(eta*dt) << "\n";
134 <  
135 <  info->scaleBox(exp(dt*eta));  
118 >
119   }
120  
121 < void NPTi::moveB( void ){
121 > template<typename T> bool NPTi<T>::etaConverged() {
122  
123 <  int i, j;
124 <  DirectionalAtom* dAtom;
142 <  double Tb[3], ji[3];
143 <  double vel[3], frc[3];
144 <  double mass;
123 >  return ( fabs(prevEta - eta) <= etaTolerance );
124 > }
125  
126 <  double instaTemp, instaPress, instaVol;
147 <  double tt2, tb2;
148 <  
149 <  tt2 = tauThermostat * tauThermostat;
150 <  tb2 = tauBarostat * tauBarostat;
126 > template<typename T> double NPTi<T>::getConservedQuantity(void){
127  
128 <  instaTemp = tStats->getTemperature();
129 <  instaPress = tStats->getPressure();
130 <  instaVol = tStats->getVolume();
128 >  double conservedQuantity;
129 >  double Energy;
130 >  double thermostat_kinetic;
131 >  double thermostat_potential;
132 >  double barostat_kinetic;
133 >  double barostat_potential;
134  
135 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
157 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
158 <                 (p_convert*NkBT*tb2));
159 <  
160 <  for( i=0; i<nAtoms; i++ ){
135 >  Energy = tStats->getTotalE();
136  
137 <    atoms[i]->getVel( vel );
138 <    atoms[i]->getFrc( frc );
137 >  thermostat_kinetic = fkBT* tt2 * chi * chi /
138 >    (2.0 * eConvert);
139  
140 <    mass = atoms[i]->getMass();
140 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
141  
167 –    // velocity half step
168 –    for (j=0; j < 3; j++)
169 –      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
170 –    
171 –    atoms[i]->setVel( vel );
142  
143 <    if( atoms[i]->isDirectional() ){
143 >  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
144 >    (2.0 * eConvert);
145  
146 <      dAtom = (DirectionalAtom *)atoms[i];
146 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
147 >    eConvert;
148  
149 <      // get and convert the torque to body frame      
149 >  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
150 >    barostat_kinetic + barostat_potential;
151  
152 <      dAtom->getTrq( Tb );
153 <      dAtom->lab2Body( Tb );
152 > //   cout.width(8);
153 > //   cout.precision(8);
154  
155 <      // get the angular momentum, and propagate a half step
156 <
157 <      dAtom->getJ( ji );
158 <
186 <      for (j=0; j < 3; j++)
187 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);    
188 <
189 <      dAtom->setJ( ji );
190 <    }
191 <  }
155 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
156 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
157 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
158 >  return conservedQuantity;
159   }
160  
161 < int NPTi::readyCheck() {
162 <
163 <  // First check to see if we have a target temperature.
164 <  // Not having one is fatal.
198 <  
199 <  if (!have_target_temp) {
200 <    sprintf( painCave.errMsg,
201 <             "NPTi error: You can't use the NPTi integrator\n"
202 <             "   without a targetTemp!\n"
203 <             );
204 <    painCave.isFatal = 1;
205 <    simError();
206 <    return -1;
207 <  }
161 > template<typename T> string NPTi<T>::getAdditionalParameters(void){
162 >  string parameters;
163 >  const int BUFFERSIZE = 2000; // size of the read buffer
164 >  char buffer[BUFFERSIZE];
165  
166 <  if (!have_target_pressure) {
167 <    sprintf( painCave.errMsg,
211 <             "NPTi error: You can't use the NPTi integrator\n"
212 <             "   without a targetPressure!\n"
213 <             );
214 <    painCave.isFatal = 1;
215 <    simError();
216 <    return -1;
217 <  }
218 <  
219 <  // We must set tauThermostat.
220 <  
221 <  if (!have_tau_thermostat) {
222 <    sprintf( painCave.errMsg,
223 <             "NPTi error: If you use the NPTi\n"
224 <             "   integrator, you must set tauThermostat.\n");
225 <    painCave.isFatal = 1;
226 <    simError();
227 <    return -1;
228 <  }    
166 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
167 >  parameters += buffer;
168  
169 <  // We must set tauBarostat.
170 <  
232 <  if (!have_tau_barostat) {
233 <    sprintf( painCave.errMsg,
234 <             "NPTi error: If you use the NPTi\n"
235 <             "   integrator, you must set tauBarostat.\n");
236 <    painCave.isFatal = 1;
237 <    simError();
238 <    return -1;
239 <  }    
169 >  sprintf(buffer,"\t%G\t0\t0;", eta);
170 >  parameters += buffer;
171  
172 <  // We need NkBT a lot, so just set it here:
172 >  sprintf(buffer,"\t0\t%G\t0;", eta);
173 >  parameters += buffer;
174  
175 <  NkBT = (double)info->ndf * kB * targetTemp;
175 >  sprintf(buffer,"\t0\t0\t%G;", eta);
176 >  parameters += buffer;
177  
178 <  return 1;
178 >  return parameters;
179 >
180   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines