OOPSE/libmdtools/ExtendedSystem.cpp

#include <math.h>
#include "Atom.hpp"
#include "Molecule.hpp"
#include "SimInfo.hpp"
#include "Thermo.hpp"
#include "ExtendedSystem.hpp"
#include "simError.h"

ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {

  // get what information we need from the SimInfo object
  
  entry_plug = the_entry_plug;
  zeta = 0.0;
  epsilonDot = 0.0;
  have_tau_thermostat = 0;
  have_tau_barostat = 0;
  have_target_temp = 0;
  have_target_pressure = 0; 
  have_qmass = 0;

}

void ExtendedSystem::NoseHooverNVT( double dt, double ke ){

  // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
  
  int i;
  double NkBT, zetaScale, ke_temp;
  double vx, vy, vz, jx, jy, jz;
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to 
                                        // amu*Ang^2*fs^-2/K
  DirectionalAtom* dAtom;    

  if (this->NVTready()) {

    atoms = entry_plug->atoms;
    
    ke_temp = ke * e_convert;
    NkBT = (double)entry_plug->ndf * kB * targetTemp;
    
    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
    // qmass is set in the parameter file
    
    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
    
    zetaScale = zeta * dt;
    
    std::cerr << "zetaScale = " << zetaScale << "\n";
    
    // perform thermostat scaling on linear velocities and angular momentum
    for(i = 0; i < entry_plug->n_atoms; i++){
      
      vx = atoms[i]->get_vx();
      vy = atoms[i]->get_vy();
      vz = atoms[i]->get_vz();
      
      atoms[i]->set_vx(vx * (1.0 - zetaScale));
      atoms[i]->set_vy(vy * (1.0 - zetaScale));
      atoms[i]->set_vz(vz * (1.0 - zetaScale));
    }
    if( entry_plug->n_oriented ){
      
      for( i=0; i < entry_plug->n_atoms; i++ ){
        
        if( atoms[i]->isDirectional() ){
          
          dAtom = (DirectionalAtom *)atoms[i];
          
          jx = dAtom->getJx();
          jy = dAtom->getJy();
          jz = dAtom->getJz();
          
          dAtom->setJx(jx * (1.0 - zetaScale));
          dAtom->setJy(jy * (1.0 - zetaScale));
          dAtom->setJz(jz * (1.0 - zetaScale));
        }
      } 
    }
  }
}


void ExtendedSystem::NoseHooverAndersonNPT( double dt, 
                                            double ke, 
                                            double p_tensor[9] ) {

  // Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 
  // Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500

  double oldBox[3];
  double newBox[3];
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  const double p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1
  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to 
                                        // amu*Ang^2*fs^-2/K

  int i;
  double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
  double volume, p_mol;
  double vx, vy, vz, jx, jy, jz;
  DirectionalAtom* dAtom;

  if (this->NPTready()) {
    atoms = entry_plug->atoms;
    
    p_ext = targetPressure * p_units;
    p_mol = (p_tensor[0] + p_tensor[4] + p_tensor[8])/3.0;
   
    entry_plug->getBox(oldBox);
    volume = oldBox[0]*oldBox[1]*oldBox[2];
    
    ke_temp = ke * e_convert;
    NkBT = (double)entry_plug->ndf * kB * targetTemp;
    
    // propagate the strain rate
    
    epsilonDot +=  dt * ((p_mol - p_ext) * volume / 
                         (tauBarostat*tauBarostat * kB * targetTemp) );
    
    // determine the change in cell volume
    scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
    std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n"; 
    
    newBox[0] = oldBox[0] * scale;
    newBox[1] = oldBox[1] * scale;
    newBox[2] = oldBox[2] * scale;
    volume = newBox[0]*newBox[1]*newBox[2];
    
    entry_plug->setBox(newBox);
    
    // perform affine transform to update positions with volume fluctuations
    this->AffineTransform( oldBox, newBox );
    
    epsilonScale = epsilonDot * dt;
    
    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin 
    // qmass is set in the parameter file
    
    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
    zetaScale = zeta * dt;
    
    std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale <<  "\n";
    
  // apply barostating and thermostating to velocities and angular momenta
    for(i = 0; i < entry_plug->n_atoms; i++){
      
      vx = atoms[i]->get_vx();
      vy = atoms[i]->get_vy();
      vz = atoms[i]->get_vz();
      
      atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
      atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
      atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
    }
    if( entry_plug->n_oriented ){
      
      for( i=0; i < entry_plug->n_atoms; i++ ){
        
        if( atoms[i]->isDirectional() ){
          
          dAtom = (DirectionalAtom *)atoms[i];
          
          jx = dAtom->getJx();
          jy = dAtom->getJy();
          jz = dAtom->getJz();
          
          dAtom->setJx( jx * (1.0 - zetaScale));
          dAtom->setJy( jy * (1.0 - zetaScale));
          dAtom->setJz( jz * (1.0 - zetaScale));
        }
      } 
    }
  }
}

void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){

  int i;
  double r[3];
  double boxNum[3];
  double percentScale[3];
  double delta[3];
  double rxi, ryi, rzi;

  molecules = entry_plug->molecules;
    
  // first determine the scaling factor from the box size change
  percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
  percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
  percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
  
  for (i=0; i < entry_plug->n_mol; i++) {
    
    molecules[i].getCOM(r);

    // find the minimum image coordinates of the molecular centers of mass:    
    
    boxNum[0] = oldBox[0] * copysign(1.0,r[0]) * 
      (double)(int)(fabs(r[0]/oldBox[0]) + 0.5);

    boxNum[1] = oldBox[1] * copysign(1.0,r[1]) * 
      (double)(int)(fabs(r[1]/oldBox[1]) + 0.5);

    boxNum[2] = oldBox[2] * copysign(1.0,r[2]) * 
      (double)(int)(fabs(r[2]/oldBox[2]) + 0.5);

    rxi = r[0] - boxNum[0];
    ryi = r[1] - boxNum[1];
    rzi = r[2] - boxNum[2];

    // update the minimum image coordinates using the scaling factor
    rxi += rxi*percentScale[0];
    ryi += ryi*percentScale[1];
    rzi += rzi*percentScale[2];

    delta[0] = r[0] - (rxi + boxNum[0]);
    delta[1] = r[1] - (ryi + boxNum[1]);
    delta[2] = r[2] - (rzi + boxNum[2]);

    molecules[i].moveCOM(delta);
  }
}

short int ExtendedSystem::NVTready() {
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  double NkBT;

  if (!have_target_temp) {
    sprintf( painCave.errMsg,
             "ExtendedSystem error: You can't use NVT without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }
    
  if (!have_qmass) {
    if (have_tau_thermostat) {

      NkBT = (double)entry_plug->ndf * kB * targetTemp;
      std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
      this->setQmass(tauThermostat * NkBT);

    } else {
      sprintf( painCave.errMsg,
               "ExtendedSystem error: If you use the constant temperature\n"
               "    ensemble, you must set either tauThermostat or qMass.\n");
      painCave.isFatal = 1;
      simError();
    }
  }

  return 1;
}

short int ExtendedSystem::NPTready() {
  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
  double NkBT;

  if (!have_target_temp) {
    sprintf( painCave.errMsg,
             "ExtendedSystem error: You can't use NPT without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  if (!have_target_pressure) {
    sprintf( painCave.errMsg,
             "ExtendedSystem error: You can't use NPT without a targetPressure!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }
    
  if (!have_tau_barostat) {
    sprintf( painCave.errMsg,
             "ExtendedSystem error: If you use the NPT\n"
             "    ensemble, you must set tauBarostat.\n");
    painCave.isFatal = 1;
    simError();
  }

  if (!have_qmass) {
    if (have_tau_thermostat) {

      NkBT = (double)entry_plug->ndf * kB * targetTemp;
      std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
      this->setQmass(tauThermostat * NkBT);

    } else {
      sprintf( painCave.errMsg,
               "ExtendedSystem error: If you use the NPT\n"
               "    ensemble, you must set either tauThermostat or qMass.\n");
      painCave.isFatal = 1;
      simError();
    }  
  }
  return 1;
}
  
Revision:	483
Committed:	Wed Apr 9 04:06:43 2003 UTC (21 years, 3 months ago) by gezelter
File size:	8792 byte(s)
Log Message:	fixes for NPT and NVT
#	User	Rev	Content
1	gezelter	453	#include <math.h>
2	gezelter	454	#include "Atom.hpp"
3			#include "Molecule.hpp"
4			#include "SimInfo.hpp"
5			#include "Thermo.hpp"
6			#include "ExtendedSystem.hpp"
7	gezelter	481	#include "simError.h"
8	gezelter	453
9	gezelter	466	ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {
10	gezelter	453
11			// get what information we need from the SimInfo object
12
13	gezelter	466	entry_plug = the_entry_plug;
14	gezelter	457	zeta = 0.0;
15			epsilonDot = 0.0;
16	gezelter	481	have_tau_thermostat = 0;
17			have_tau_barostat = 0;
18			have_target_temp = 0;
19			have_target_pressure = 0;
20			have_qmass = 0;
21
22	gezelter	453	}
23
24	gezelter	457	void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
25	gezelter	453
26			// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
27
28	gezelter	454	int i;
29	gezelter	457	double NkBT, zetaScale, ke_temp;
30	gezelter	454	double vx, vy, vz, jx, jy, jz;
31	gezelter	457	const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
32			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
33			// amuAng^2fs^-2/K
34	gezelter	458	DirectionalAtom* dAtom;
35
36	gezelter	481	if (this->NVTready()) {
37	gezelter	453
38	gezelter	481	atoms = entry_plug->atoms;
39	gezelter	454
40	gezelter	481	ke_temp = ke * e_convert;
41			NkBT = (double)entry_plug->ndf * kB * targetTemp;
42	gezelter	454
43	gezelter	481	// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
44			// qmass is set in the parameter file
45
46			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
47
48			zetaScale = zeta * dt;
49
50			std::cerr << "zetaScale = " << zetaScale << "\n";
51
52			// perform thermostat scaling on linear velocities and angular momentum
53			for(i = 0; i < entry_plug->n_atoms; i++){
54	gezelter	454
55	gezelter	481	vx = atoms[i]->get_vx();
56			vy = atoms[i]->get_vy();
57			vz = atoms[i]->get_vz();
58
59			atoms[i]->set_vx(vx * (1.0 - zetaScale));
60			atoms[i]->set_vy(vy * (1.0 - zetaScale));
61			atoms[i]->set_vz(vz * (1.0 - zetaScale));
62			}
63			if( entry_plug->n_oriented ){
64
65			for( i=0; i < entry_plug->n_atoms; i++ ){
66	gezelter	454
67	gezelter	481	if( atoms[i]->isDirectional() ){
68
69			dAtom = (DirectionalAtom *)atoms[i];
70
71			jx = dAtom->getJx();
72			jy = dAtom->getJy();
73			jz = dAtom->getJz();
74
75			dAtom->setJx(jx * (1.0 - zetaScale));
76			dAtom->setJy(jy * (1.0 - zetaScale));
77			dAtom->setJz(jz * (1.0 - zetaScale));
78			}
79			}
80			}
81	gezelter	454	}
82	gezelter	453	}
83
84
85	gezelter	457	void ExtendedSystem::NoseHooverAndersonNPT( double dt,
86			double ke,
87	gezelter	483	double p_tensor[9] ) {
88	gezelter	453
89			// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
90			// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
91
92	gezelter	457	double oldBox[3];
93			double newBox[3];
94			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
95			const double p_units = 6.10192996e-9; // converts atm to amufs^-2Ang^-1
96			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
97			// amuAng^2fs^-2/K
98	gezelter	453
99	gezelter	474	int i;
100	gezelter	458	double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
101			double volume, p_mol;
102			double vx, vy, vz, jx, jy, jz;
103			DirectionalAtom* dAtom;
104	gezelter	453
105	gezelter	481	if (this->NPTready()) {
106			atoms = entry_plug->atoms;
107	gezelter	454
108	gezelter	481	p_ext = targetPressure * p_units;
109	gezelter	483	p_mol = (p_tensor[0] + p_tensor[4] + p_tensor[8])/3.0;
110
111	gezelter	481	entry_plug->getBox(oldBox);
112			volume = oldBox[0]oldBox[1]oldBox[2];
113	gezelter	454
114	gezelter	481	ke_temp = ke * e_convert;
115			NkBT = (double)entry_plug->ndf * kB * targetTemp;
116
117	gezelter	483	// propagate the strain rate
118	gezelter	481
119			epsilonDot += dt * ((p_mol - p_ext) * volume /
120			(tauBarostattauBarostat kB * targetTemp) );
121
122			// determine the change in cell volume
123			scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
124	gezelter	483	std::cerr << "pmol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n";
125	gezelter	481
126			newBox[0] = oldBox[0] * scale;
127			newBox[1] = oldBox[1] * scale;
128			newBox[2] = oldBox[2] * scale;
129			volume = newBox[0]newBox[1]newBox[2];
130
131			entry_plug->setBox(newBox);
132
133			// perform affine transform to update positions with volume fluctuations
134			this->AffineTransform( oldBox, newBox );
135
136			epsilonScale = epsilonDot * dt;
137
138			// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
139			// qmass is set in the parameter file
140
141			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
142			zetaScale = zeta * dt;
143
144			std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale << "\n";
145
146			// apply barostating and thermostating to velocities and angular momenta
147			for(i = 0; i < entry_plug->n_atoms; i++){
148	gezelter	454
149	gezelter	481	vx = atoms[i]->get_vx();
150			vy = atoms[i]->get_vy();
151			vz = atoms[i]->get_vz();
152
153			atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
154			atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
155			atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
156			}
157			if( entry_plug->n_oriented ){
158
159			for( i=0; i < entry_plug->n_atoms; i++ ){
160	gezelter	454
161	gezelter	481	if( atoms[i]->isDirectional() ){
162
163			dAtom = (DirectionalAtom *)atoms[i];
164
165			jx = dAtom->getJx();
166			jy = dAtom->getJy();
167			jz = dAtom->getJz();
168
169			dAtom->setJx( jx * (1.0 - zetaScale));
170			dAtom->setJy( jy * (1.0 - zetaScale));
171			dAtom->setJz( jz * (1.0 - zetaScale));
172			}
173			}
174			}
175	gezelter	454	}
176	gezelter	453	}
177
178	gezelter	457	void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
179	gezelter	453
180			int i;
181	gezelter	457	double r[3];
182			double boxNum[3];
183			double percentScale[3];
184	gezelter	476	double delta[3];
185	gezelter	457	double rxi, ryi, rzi;
186	gezelter	474
187			molecules = entry_plug->molecules;
188	gezelter	453
189			// first determine the scaling factor from the box size change
190	gezelter	457	percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
191			percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
192			percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
193	gezelter	453
194	gezelter	474	for (i=0; i < entry_plug->n_mol; i++) {
195	gezelter	453
196	gezelter	458	molecules[i].getCOM(r);
197	gezelter	475
198	gezelter	457	// find the minimum image coordinates of the molecular centers of mass:
199	gezelter	453
200	gezelter	457	boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
201			(double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
202	gezelter	453
203	gezelter	457	boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
204			(double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
205	gezelter	453
206	gezelter	457	boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
207			(double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
208	gezelter	453
209	gezelter	457	rxi = r[0] - boxNum[0];
210			ryi = r[1] - boxNum[1];
211			rzi = r[2] - boxNum[2];
212
213	gezelter	453	// update the minimum image coordinates using the scaling factor
214	gezelter	457	rxi += rxi*percentScale[0];
215			ryi += ryi*percentScale[1];
216			rzi += rzi*percentScale[2];
217	gezelter	453
218	gezelter	476	delta[0] = r[0] - (rxi + boxNum[0]);
219			delta[1] = r[1] - (ryi + boxNum[1]);
220			delta[2] = r[2] - (rzi + boxNum[2]);
221	gezelter	457
222	gezelter	476	molecules[i].moveCOM(delta);
223	gezelter	453	}
224			}
225	gezelter	481
226			short int ExtendedSystem::NVTready() {
227			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
228			double NkBT;
229
230			if (!have_target_temp) {
231			sprintf( painCave.errMsg,
232			"ExtendedSystem error: You can't use NVT without a targetTemp!\n"
233			);
234			painCave.isFatal = 1;
235			simError();
236			return -1;
237			}
238
239			if (!have_qmass) {
240			if (have_tau_thermostat) {
241
242			NkBT = (double)entry_plug->ndf * kB * targetTemp;
243			std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
244			this->setQmass(tauThermostat * NkBT);
245
246			} else {
247			sprintf( painCave.errMsg,
248			"ExtendedSystem error: If you use the constant temperature\n"
249			" ensemble, you must set either tauThermostat or qMass.\n");
250			painCave.isFatal = 1;
251			simError();
252			}
253			}
254
255	gezelter	483	return 1;
256	gezelter	481	}
257
258			short int ExtendedSystem::NPTready() {
259			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
260			double NkBT;
261
262			if (!have_target_temp) {
263			sprintf( painCave.errMsg,
264			"ExtendedSystem error: You can't use NPT without a targetTemp!\n"
265			);
266			painCave.isFatal = 1;
267			simError();
268			return -1;
269			}
270
271			if (!have_target_pressure) {
272			sprintf( painCave.errMsg,
273			"ExtendedSystem error: You can't use NPT without a targetPressure!\n"
274			);
275			painCave.isFatal = 1;
276			simError();
277			return -1;
278			}
279
280			if (!have_tau_barostat) {
281			sprintf( painCave.errMsg,
282			"ExtendedSystem error: If you use the NPT\n"
283			" ensemble, you must set tauBarostat.\n");
284			painCave.isFatal = 1;
285			simError();
286			}
287
288			if (!have_qmass) {
289			if (have_tau_thermostat) {
290
291			NkBT = (double)entry_plug->ndf * kB * targetTemp;
292			std::cerr << "Setting qMass = " << tauThermostat * NkBT << "\n";
293			this->setQmass(tauThermostat * NkBT);
294
295			} else {
296			sprintf( painCave.errMsg,
297			"ExtendedSystem error: If you use the NPT\n"
298			" ensemble, you must set either tauThermostat or qMass.\n");
299			painCave.isFatal = 1;
300			simError();
301			}
302			}
303	gezelter	483	return 1;
304	gezelter	481	}
305