OOPSE/libmdtools/ExtendedSystem.cpp

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

ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {

  // get what information we need from the SimInfo object
  
  entry_plug = the_entry_plug;
  nAtoms = entry_plug->n_atoms;
  atoms = entry_plug->atoms;
  nMols = entry_plug->n_mol;
  molecules = entry_plug->molecules;
  nOriented = entry_plug->n_oriented;
  ndf = entry_plug->ndf;
  zeta = 0.0;
  epsilonDot = 0.0;

}

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;    

  ke_temp = ke * e_convert;
  NkBT = (double)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 );
  std::cerr << "ke_temp = " << ke_temp << "\n";

  zetaScale = zeta * dt;
  

  // perform thermostat scaling on linear velocities and angular momentum
  for(i = 0; i < nAtoms; 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( nOriented ){
    
    for( i=0; i < nAtoms; 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_int ) {

  // 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

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

  p_ext = targetPressure * p_units;
  p_mol = p_int * p_units;

  entry_plug->getBox(oldBox);

  volume = oldBox[0]*oldBox[1]*oldBox[2];

  ke_temp = ke * e_convert;
  NkBT = (double)ndf * kB * targetTemp;

  // propogate the strain rate

  epsilonDot +=  dt * ((p_mol - p_ext) * volume / 
                       (tauRelax*tauRelax * kB * targetTemp) );

  // determine the change in cell volume
  scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));

  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;
  
  // apply barostating and thermostating to velocities and angular momenta
  for(i = 0; i < nAtoms; 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( nOriented ){
    
    for( i=0; i < nAtoms; 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 rxi, ryi, rzi;
    
  // 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 < nMols; 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];

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

    molecules[i].moveCOM(r);
  }
}
Revision:	471
Committed:	Mon Apr 7 20:51:59 2003 UTC (21 years, 3 months ago) by gezelter
File size:	5806 byte(s)
Log Message:	Working on 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	453
8	gezelter	466	ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {
9	gezelter	453
10			// get what information we need from the SimInfo object
11
12	gezelter	466	entry_plug = the_entry_plug;
13	gezelter	458	nAtoms = entry_plug->n_atoms;
14			atoms = entry_plug->atoms;
15			nMols = entry_plug->n_mol;
16			molecules = entry_plug->molecules;
17			nOriented = entry_plug->n_oriented;
18			ndf = entry_plug->ndf;
19	gezelter	457	zeta = 0.0;
20			epsilonDot = 0.0;
21	gezelter	453
22			}
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	457	ke_temp = ke * e_convert;
37	gezelter	458	NkBT = (double)ndf * kB * targetTemp;
38	gezelter	453
39	gezelter	457	// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
40	gezelter	453	// qmass is set in the parameter file
41	gezelter	457
42			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
43	gezelter	471	std::cerr << "ke_temp = " << ke_temp << "\n";
44
45	gezelter	453	zetaScale = zeta * dt;
46	gezelter	471
47	gezelter	453
48	gezelter	471
49	gezelter	453	// perform thermostat scaling on linear velocities and angular momentum
50	gezelter	458	for(i = 0; i < nAtoms; i++){
51	gezelter	454
52			vx = atoms[i]->get_vx();
53			vy = atoms[i]->get_vy();
54			vz = atoms[i]->get_vz();
55
56	gezelter	457	atoms[i]->set_vx(vx * (1.0 - zetaScale));
57			atoms[i]->set_vy(vy * (1.0 - zetaScale));
58			atoms[i]->set_vz(vz * (1.0 - zetaScale));
59	gezelter	453	}
60	gezelter	458	if( nOriented ){
61	gezelter	454
62	gezelter	458	for( i=0; i < nAtoms; i++ ){
63	gezelter	454
64			if( atoms[i]->isDirectional() ){
65
66			dAtom = (DirectionalAtom *)atoms[i];
67
68			jx = dAtom->getJx();
69			jy = dAtom->getJy();
70			jz = dAtom->getJz();
71
72	gezelter	457	dAtom->setJx(jx * (1.0 - zetaScale));
73			dAtom->setJy(jy * (1.0 - zetaScale));
74			dAtom->setJz(jz * (1.0 - zetaScale));
75	gezelter	454	}
76			}
77			}
78	gezelter	453	}
79
80
81	gezelter	457	void ExtendedSystem::NoseHooverAndersonNPT( double dt,
82			double ke,
83			double p_int ) {
84	gezelter	453
85			// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
86			// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
87
88	gezelter	457	double oldBox[3];
89			double newBox[3];
90			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
91			const double p_units = 6.10192996e-9; // converts atm to amufs^-2Ang^-1
92			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
93			// amuAng^2fs^-2/K
94	gezelter	453
95	gezelter	458	double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
96			double volume, p_mol;
97			double vx, vy, vz, jx, jy, jz;
98			DirectionalAtom* dAtom;
99			int i;
100	gezelter	453
101	gezelter	457	p_ext = targetPressure * p_units;
102			p_mol = p_int * p_units;
103	gezelter	453
104	gezelter	458	entry_plug->getBox(oldBox);
105	gezelter	457
106			volume = oldBox[0]oldBox[1]oldBox[2];
107
108			ke_temp = ke * e_convert;
109	gezelter	458	NkBT = (double)ndf * kB * targetTemp;
110	gezelter	457
111	gezelter	453	// propogate the strain rate
112
113	gezelter	457	epsilonDot += dt * ((p_mol - p_ext) * volume /
114			(tauRelaxtauRelax kB * targetTemp) );
115	gezelter	453
116			// determine the change in cell volume
117	gezelter	457	scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
118	gezelter	453
119	gezelter	457	newBox[0] = oldBox[0] * scale;
120			newBox[1] = oldBox[1] * scale;
121			newBox[2] = oldBox[2] * scale;
122			volume = newBox[0]newBox[1]newBox[2];
123	gezelter	453
124	gezelter	458	entry_plug->setBox(newBox);
125
126	gezelter	453	// perform affine transform to update positions with volume fluctuations
127	gezelter	457	this->AffineTransform( oldBox, newBox );
128	gezelter	453
129	gezelter	454	epsilonScale = epsilonDot * dt;
130	gezelter	453
131			// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
132			// qmass is set in the parameter file
133	gezelter	457
134			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
135	gezelter	453	zetaScale = zeta * dt;
136
137			// apply barostating and thermostating to velocities and angular momenta
138	gezelter	458	for(i = 0; i < nAtoms; i++){
139	gezelter	454
140			vx = atoms[i]->get_vx();
141			vy = atoms[i]->get_vy();
142			vz = atoms[i]->get_vz();
143
144	gezelter	457	atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
145			atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
146			atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
147	gezelter	453	}
148	gezelter	458	if( nOriented ){
149	gezelter	454
150	gezelter	458	for( i=0; i < nAtoms; i++ ){
151	gezelter	454
152			if( atoms[i]->isDirectional() ){
153
154			dAtom = (DirectionalAtom *)atoms[i];
155
156			jx = dAtom->getJx();
157			jy = dAtom->getJy();
158			jz = dAtom->getJz();
159
160			dAtom->setJx( jx * (1.0 - zetaScale));
161			dAtom->setJy( jy * (1.0 - zetaScale));
162			dAtom->setJz( jz * (1.0 - zetaScale));
163			}
164			}
165			}
166	gezelter	453	}
167
168	gezelter	457	void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
169	gezelter	453
170			int i;
171	gezelter	457	double r[3];
172			double boxNum[3];
173			double percentScale[3];
174			double rxi, ryi, rzi;
175	gezelter	453
176			// first determine the scaling factor from the box size change
177	gezelter	457	percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
178			percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
179			percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
180	gezelter	453
181			for (i=0; i < nMols; i++) {
182
183	gezelter	458	molecules[i].getCOM(r);
184	gezelter	453
185	gezelter	457	// find the minimum image coordinates of the molecular centers of mass:
186	gezelter	453
187	gezelter	457	boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
188			(double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
189	gezelter	453
190	gezelter	457	boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
191			(double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
192	gezelter	453
193	gezelter	457	boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
194			(double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
195	gezelter	453
196	gezelter	457	rxi = r[0] - boxNum[0];
197			ryi = r[1] - boxNum[1];
198			rzi = r[2] - boxNum[2];
199
200	gezelter	453	// update the minimum image coordinates using the scaling factor
201	gezelter	457	rxi += rxi*percentScale[0];
202			ryi += ryi*percentScale[1];
203			rzi += rzi*percentScale[2];
204	gezelter	453
205	gezelter	457	r[0] = rxi + boxNum[0];
206			r[1] = ryi + boxNum[1];
207			r[2] = rzi + boxNum[2];
208
209	gezelter	458	molecules[i].moveCOM(r);
210	gezelter	453	}
211			}