OOPSE/libmdtools/NPTim.cpp

#include <cmath>
#include "Atom.hpp"
#include "Molecule.hpp"
#include "SRI.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"
#include "ForceFields.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "Integrator.hpp"
#include "simError.h" 


// Basic isotropic thermostating and barostating via the Melchionna
// modification of the Hoover algorithm:
//
//    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
//       Molec. Phys., 78, 533. 
//
//           and
// 
//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.

//  The NPTim variant scales the molecular center-of-mass coordinates
//  instead of the atomic coordinates

NPTim::NPTim ( SimInfo *theInfo, ForceFields* the_ff):
  Integrator( theInfo, the_ff )
{
  chi = 0.0;
  eta = 0.0;
  have_tau_thermostat = 0;
  have_tau_barostat = 0;
  have_target_temp = 0;
  have_target_pressure = 0;
}

void NPTim::moveA() {
  
  int i, j, k;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double A[3][3], I[3][3];
  double angle, mass;
  double vel[3], pos[3], frc[3];

  double rj[3];
  double instaTemp, instaPress, instaVol;
  double tt2, tb2, scaleFactor;

  int nInMol;
  double rc[3];

  nMols = info->n_mol;
  myMolecules = info->molecules;

  tt2 = tauThermostat * tauThermostat;
  tb2 = tauBarostat * tauBarostat;

  instaTemp = tStats->getTemperature();
  instaPress = tStats->getPressure();
  instaVol = tStats->getVolume();
   
   // first evolve chi a half step
  
  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
                 (p_convert*NkBT*tb2));

  for( i = 0; i < nMols; i++) {

    myMolecules[i].getCOM(rc);

    nInMol = myMolecules[i].getNAtoms();
    myAtoms = myMolecules[i].getMyAtoms();

    // find the minimum image coordinates of the molecular centers of mass:

    info->wrapVector(rc);

    for (j = 0; j < nInMol; j++) {

      if(myAtoms[j] != NULL) {

        myAtoms[j]->getVel( vel );
        myAtoms[j]->getPos( pos );
        myAtoms[j]->getFrc( frc );

        mass = myAtoms[j]->getMass();

        for (k=0; k < 3; k++)
          vel[k] += dt2 * ((frc[k] / mass ) * eConvert - vel[k]*(chi+eta));

        myAtoms[j]->setVel( vel );

        for (k = 0; k < 3; k++) 
          pos[k] += dt * (vel[k] + eta*rc[k]);

        myAtoms[j]->setPos( pos );

        if( myAtoms[j]->isDirectional() ){

          dAtom = (DirectionalAtom *)myAtoms[j];
          
          // get and convert the torque to body frame
      
          dAtom->getTrq( Tb );
          dAtom->lab2Body( Tb );
      
          // get the angular momentum, and propagate a half step
          
          dAtom->getJ( ji );

          for (k=0; k < 3; k++) 
            ji[k] += dt2 * (Tb[k] * eConvert - ji[k]*chi);
          
          // use the angular velocities to propagate the rotation matrix a
          // full time step
          
          dAtom->getA(A);
          dAtom->getI(I);
          
          // rotate about the x-axis      
          angle = dt2 * ji[0] / I[0][0];
          this->rotate( 1, 2, angle, ji, A ); 
          
          // rotate about the y-axis
          angle = dt2 * ji[1] / I[1][1];
          this->rotate( 2, 0, angle, ji, A );
          
          // rotate about the z-axis
          angle = dt * ji[2] / I[2][2];
          this->rotate( 0, 1, angle, ji, A);
          
          // rotate about the y-axis
          angle = dt2 * ji[1] / I[1][1];
          this->rotate( 2, 0, angle, ji, A );
          
          // rotate about the x-axis
          angle = dt2 * ji[0] / I[0][0];
          this->rotate( 1, 2, angle, ji, A );
          
          dAtom->setJ( ji );
          dAtom->setA( A  );    
        }                        
      }
    }
  }

  // Scale the box after all the positions have been moved:
  
  scaleFactor = exp(dt*eta);

  if (scaleFactor > 1.1 || scaleFactor < 0.9) {
    sprintf( painCave.errMsg,
             "NPTi error: Attempting a Box scaling of more than 10 percent"
             " check your tauBarostat, as it is probably too small!\n"
             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
             );
    painCave.isFatal = 1;
    simError();
  } else {         
    info->scaleBox(exp(dt*eta));      
  }
}

void NPTim::moveB( void ){
  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double vel[3], frc[3];
  double mass;

  double instaTemp, instaPress, instaVol;
  double tt2, tb2;
 
  tt2 = tauThermostat * tauThermostat;
  tb2 = tauBarostat * tauBarostat;

  instaTemp = tStats->getTemperature();
  instaPress = tStats->getPressure();
  instaVol = tStats->getVolume();

  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
  eta += dt2 * ( instaVol * (instaPress - targetPressure) / 
                 (p_convert*NkBT*tb2));
  
  for( i=0; i<nAtoms; i++ ){
    
    atoms[i]->getVel( vel );
    atoms[i]->getFrc( frc );
    
    mass = atoms[i]->getMass();
    
    // velocity half step
    for (j=0; j < 3; j++) 
      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
    
    atoms[i]->setVel( vel );
    
    if( atoms[i]->isDirectional() ){
      
      dAtom = (DirectionalAtom *)atoms[i];
      
      // get and convert the torque to body frame      
      
      dAtom->getTrq( Tb );
      dAtom->lab2Body( Tb );
      
      // get the angular momentum, and propagate a half step
      
      dAtom->getJ( ji );
      
      for (j=0; j < 3; j++) 
        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);     
      
      dAtom->setJ( ji );
    }
  }
}

int NPTim::readyCheck() {
 
  // First check to see if we have a target temperature. 
  // Not having one is fatal. 
  
  if (!have_target_temp) {
    sprintf( painCave.errMsg,
             "NPTim error: You can't use the NPTim integrator\n"
             "   without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  if (!have_target_pressure) {
    sprintf( painCave.errMsg,
             "NPTim error: You can't use the NPTim integrator\n"
             "   without a targetPressure!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }
  
  // We must set tauThermostat.
   
  if (!have_tau_thermostat) {
    sprintf( painCave.errMsg,
             "NPTim error: If you use the NPTim\n"
             "   integrator, you must set tauThermostat.\n");
    painCave.isFatal = 1;
    simError();
    return -1;
  }    

  // We must set tauBarostat.
   
  if (!have_tau_barostat) {
    sprintf( painCave.errMsg,
             "NPTim error: If you use the NPTim\n"
             "   integrator, you must set tauBarostat.\n");
    painCave.isFatal = 1;
    simError();
    return -1;
  }    

  // We need NkBT a lot, so just set it here:

  NkBT = (double)info->ndf * kB * targetTemp;

  return 1;
}
Revision:	611
Committed:	Tue Jul 15 17:10:50 2003 UTC (20 years, 11 months ago) by gezelter
File size:	6780 byte(s)
Log Message:	Fixing pressure tensor
#	User	Rev	Content
1	gezelter	596	#include <cmath>
2			#include "Atom.hpp"
3	gezelter	604	#include "Molecule.hpp"
4	gezelter	596	#include "SRI.hpp"
5			#include "AbstractClasses.hpp"
6			#include "SimInfo.hpp"
7			#include "ForceFields.hpp"
8			#include "Thermo.hpp"
9			#include "ReadWrite.hpp"
10			#include "Integrator.hpp"
11			#include "simError.h"
12
13
14			// Basic isotropic thermostating and barostating via the Melchionna
15			// modification of the Hoover algorithm:
16			//
17			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
18			// Molec. Phys., 78, 533.
19			//
20			// and
21			//
22			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
23
24			// The NPTim variant scales the molecular center-of-mass coordinates
25			// instead of the atomic coordinates
26
27			NPTim::NPTim ( SimInfo theInfo, ForceFields the_ff):
28			Integrator( theInfo, the_ff )
29			{
30			chi = 0.0;
31			eta = 0.0;
32			have_tau_thermostat = 0;
33			have_tau_barostat = 0;
34			have_target_temp = 0;
35			have_target_pressure = 0;
36			}
37
38			void NPTim::moveA() {
39
40	gezelter	605	int i, j, k;
41	gezelter	596	DirectionalAtom* dAtom;
42	gezelter	604	double Tb[3], ji[3];
43			double A[3][3], I[3][3];
44			double angle, mass;
45			double vel[3], pos[3], frc[3];
46
47			double rj[3];
48	gezelter	596	double instaTemp, instaPress, instaVol;
49	gezelter	611	double tt2, tb2, scaleFactor;
50	gezelter	596
51	gezelter	604	int nInMol;
52			double rc[3];
53
54	gezelter	596	nMols = info->n_mol;
55	gezelter	604	myMolecules = info->molecules;
56	gezelter	596
57			tt2 = tauThermostat * tauThermostat;
58			tb2 = tauBarostat * tauBarostat;
59
60			instaTemp = tStats->getTemperature();
61			instaPress = tStats->getPressure();
62			instaVol = tStats->getVolume();
63
64			// first evolve chi a half step
65
66			chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
67			eta += dt2 * ( instaVol * (instaPress - targetPressure) /
68			(p_convertNkBTtb2));
69
70			for( i = 0; i < nMols; i++) {
71
72	gezelter	604	myMolecules[i].getCOM(rc);
73	gezelter	596
74	gezelter	604	nInMol = myMolecules[i].getNAtoms();
75			myAtoms = myMolecules[i].getMyAtoms();
76	gezelter	596
77			// find the minimum image coordinates of the molecular centers of mass:
78
79			info->wrapVector(rc);
80
81			for (j = 0; j < nInMol; j++) {
82
83	gezelter	604	if(myAtoms[j] != NULL) {
84	gezelter	596
85	gezelter	605	myAtoms[j]->getVel( vel );
86			myAtoms[j]->getPos( pos );
87			myAtoms[j]->getFrc( frc );
88	gezelter	596
89	gezelter	605	mass = myAtoms[j]->getMass();
90	gezelter	596
91	gezelter	605	for (k=0; k < 3; k++)
92			vel[k] += dt2 * ((frc[k] / mass ) * eConvert - vel[k]*(chi+eta));
93	gezelter	596
94	gezelter	605	myAtoms[j]->setVel( vel );
95	gezelter	596
96	gezelter	605	for (k = 0; k < 3; k++)
97			pos[k] += dt * (vel[k] + eta*rc[k]);
98	gezelter	596
99	gezelter	605	myAtoms[j]->setPos( pos );
100	gezelter	596
101	gezelter	604	if( myAtoms[j]->isDirectional() ){
102	gezelter	596
103	gezelter	604	dAtom = (DirectionalAtom *)myAtoms[j];
104	gezelter	596
105			// get and convert the torque to body frame
106	gezelter	604
107			dAtom->getTrq( Tb );
108	gezelter	596	dAtom->lab2Body( Tb );
109	gezelter	604
110	gezelter	596	// get the angular momentum, and propagate a half step
111
112	gezelter	604	dAtom->getJ( ji );
113
114	gezelter	605	for (k=0; k < 3; k++)
115			ji[k] += dt2 * (Tb[k] * eConvert - ji[k]*chi);
116	gezelter	596
117			// use the angular velocities to propagate the rotation matrix a
118			// full time step
119
120	gezelter	604	dAtom->getA(A);
121			dAtom->getI(I);
122
123	gezelter	596	// rotate about the x-axis
124	gezelter	604	angle = dt2 * ji[0] / I[0][0];
125			this->rotate( 1, 2, angle, ji, A );
126	gezelter	596
127			// rotate about the y-axis
128	gezelter	604	angle = dt2 * ji[1] / I[1][1];
129			this->rotate( 2, 0, angle, ji, A );
130	gezelter	596
131			// rotate about the z-axis
132	gezelter	604	angle = dt * ji[2] / I[2][2];
133			this->rotate( 0, 1, angle, ji, A);
134	gezelter	596
135			// rotate about the y-axis
136	gezelter	604	angle = dt2 * ji[1] / I[1][1];
137			this->rotate( 2, 0, angle, ji, A );
138	gezelter	596
139			// rotate about the x-axis
140	gezelter	604	angle = dt2 * ji[0] / I[0][0];
141			this->rotate( 1, 2, angle, ji, A );
142	gezelter	596
143	gezelter	604	dAtom->setJ( ji );
144			dAtom->setA( A );
145			}
146	gezelter	596	}
147			}
148			}
149	gezelter	611
150	gezelter	596	// Scale the box after all the positions have been moved:
151
152	gezelter	611	scaleFactor = exp(dt*eta);
153
154			if (scaleFactor > 1.1 \|\| scaleFactor < 0.9) {
155			sprintf( painCave.errMsg,
156			"NPTi error: Attempting a Box scaling of more than 10 percent"
157			" check your tauBarostat, as it is probably too small!\n"
158			" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
159			);
160			painCave.isFatal = 1;
161			simError();
162			} else {
163			info->scaleBox(exp(dt*eta));
164			}
165	gezelter	596	}
166
167	gezelter	604	void NPTim::moveB( void ){
168			int i, j;
169	gezelter	596	DirectionalAtom* dAtom;
170	gezelter	604	double Tb[3], ji[3];
171			double vel[3], frc[3];
172			double mass;
173
174	gezelter	596	double instaTemp, instaPress, instaVol;
175			double tt2, tb2;
176	gezelter	604
177	gezelter	596	tt2 = tauThermostat * tauThermostat;
178			tb2 = tauBarostat * tauBarostat;
179
180			instaTemp = tStats->getTemperature();
181			instaPress = tStats->getPressure();
182			instaVol = tStats->getVolume();
183
184			chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
185			eta += dt2 * ( instaVol * (instaPress - targetPressure) /
186			(p_convertNkBTtb2));
187
188			for( i=0; i<nAtoms; i++ ){
189
190	gezelter	604	atoms[i]->getVel( vel );
191			atoms[i]->getFrc( frc );
192
193			mass = atoms[i]->getMass();
194
195	gezelter	596	// velocity half step
196	gezelter	604	for (j=0; j < 3; j++)
197			vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
198	gezelter	596
199	gezelter	604	atoms[i]->setVel( vel );
200
201	gezelter	596	if( atoms[i]->isDirectional() ){
202
203			dAtom = (DirectionalAtom *)atoms[i];
204
205	gezelter	604	// get and convert the torque to body frame
206	gezelter	596
207	gezelter	604	dAtom->getTrq( Tb );
208	gezelter	596	dAtom->lab2Body( Tb );
209
210	gezelter	604	// get the angular momentum, and propagate a half step
211	gezelter	596
212	gezelter	604	dAtom->getJ( ji );
213	gezelter	596
214	gezelter	604	for (j=0; j < 3; j++)
215			ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
216	gezelter	596
217	gezelter	604	dAtom->setJ( ji );
218	gezelter	596	}
219			}
220			}
221
222	gezelter	604	int NPTim::readyCheck() {
223	gezelter	596
224			// First check to see if we have a target temperature.
225			// Not having one is fatal.
226
227			if (!have_target_temp) {
228			sprintf( painCave.errMsg,
229	gezelter	604	"NPTim error: You can't use the NPTim integrator\n"
230	gezelter	596	" without a targetTemp!\n"
231			);
232			painCave.isFatal = 1;
233			simError();
234			return -1;
235			}
236
237			if (!have_target_pressure) {
238			sprintf( painCave.errMsg,
239	gezelter	604	"NPTim error: You can't use the NPTim integrator\n"
240	gezelter	596	" without a targetPressure!\n"
241			);
242			painCave.isFatal = 1;
243			simError();
244			return -1;
245			}
246
247			// We must set tauThermostat.
248
249			if (!have_tau_thermostat) {
250			sprintf( painCave.errMsg,
251	gezelter	604	"NPTim error: If you use the NPTim\n"
252	gezelter	596	" integrator, you must set tauThermostat.\n");
253			painCave.isFatal = 1;
254			simError();
255			return -1;
256			}
257
258			// We must set tauBarostat.
259
260			if (!have_tau_barostat) {
261			sprintf( painCave.errMsg,
262	gezelter	604	"NPTim error: If you use the NPTim\n"
263	gezelter	596	" integrator, you must set tauBarostat.\n");
264			painCave.isFatal = 1;
265			simError();
266			return -1;
267			}
268
269			// We need NkBT a lot, so just set it here:
270
271			NkBT = (double)info->ndf * kB * targetTemp;
272
273			return 1;
274			}