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 );
  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:	468
Committed:	Mon Apr 7 16:56:38 2003 UTC (21 years, 3 months ago) by gezelter
File size:	5753 byte(s)
Log Message:	Many fixes to add extended system
#	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	453	zetaScale = zeta * dt;
44
45			// perform thermostat scaling on linear velocities and angular momentum
46	gezelter	458	for(i = 0; i < nAtoms; i++){
47	gezelter	454
48			vx = atoms[i]->get_vx();
49			vy = atoms[i]->get_vy();
50			vz = atoms[i]->get_vz();
51
52	gezelter	457	atoms[i]->set_vx(vx * (1.0 - zetaScale));
53			atoms[i]->set_vy(vy * (1.0 - zetaScale));
54			atoms[i]->set_vz(vz * (1.0 - zetaScale));
55	gezelter	453	}
56	gezelter	458	if( nOriented ){
57	gezelter	454
58	gezelter	458	for( i=0; i < nAtoms; i++ ){
59	gezelter	454
60			if( atoms[i]->isDirectional() ){
61
62			dAtom = (DirectionalAtom *)atoms[i];
63
64			jx = dAtom->getJx();
65			jy = dAtom->getJy();
66			jz = dAtom->getJz();
67
68	gezelter	457	dAtom->setJx(jx * (1.0 - zetaScale));
69			dAtom->setJy(jy * (1.0 - zetaScale));
70			dAtom->setJz(jz * (1.0 - zetaScale));
71	gezelter	454	}
72			}
73			}
74	gezelter	453	}
75
76
77	gezelter	457	void ExtendedSystem::NoseHooverAndersonNPT( double dt,
78			double ke,
79			double p_int ) {
80	gezelter	453
81			// Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
82			// Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
83
84	gezelter	457	double oldBox[3];
85			double newBox[3];
86			const double kB = 8.31451e-7; // boltzmann constant in amuAng^2fs^-2/K
87			const double p_units = 6.10192996e-9; // converts atm to amufs^-2Ang^-1
88			const double e_convert = 4.184e-4; // to convert ke from kcal/mol to
89			// amuAng^2fs^-2/K
90	gezelter	453
91	gezelter	458	double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
92			double volume, p_mol;
93			double vx, vy, vz, jx, jy, jz;
94			DirectionalAtom* dAtom;
95			int i;
96	gezelter	453
97	gezelter	457	p_ext = targetPressure * p_units;
98			p_mol = p_int * p_units;
99	gezelter	453
100	gezelter	458	entry_plug->getBox(oldBox);
101	gezelter	457
102			volume = oldBox[0]oldBox[1]oldBox[2];
103
104			ke_temp = ke * e_convert;
105	gezelter	458	NkBT = (double)ndf * kB * targetTemp;
106	gezelter	457
107	gezelter	453	// propogate the strain rate
108
109	gezelter	457	epsilonDot += dt * ((p_mol - p_ext) * volume /
110			(tauRelaxtauRelax kB * targetTemp) );
111	gezelter	453
112			// determine the change in cell volume
113	gezelter	457	scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
114	gezelter	453
115	gezelter	457	newBox[0] = oldBox[0] * scale;
116			newBox[1] = oldBox[1] * scale;
117			newBox[2] = oldBox[2] * scale;
118			volume = newBox[0]newBox[1]newBox[2];
119	gezelter	453
120	gezelter	458	entry_plug->setBox(newBox);
121
122	gezelter	453	// perform affine transform to update positions with volume fluctuations
123	gezelter	457	this->AffineTransform( oldBox, newBox );
124	gezelter	453
125	gezelter	454	epsilonScale = epsilonDot * dt;
126	gezelter	453
127			// advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
128			// qmass is set in the parameter file
129	gezelter	457
130			zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
131	gezelter	453	zetaScale = zeta * dt;
132
133			// apply barostating and thermostating to velocities and angular momenta
134	gezelter	458	for(i = 0; i < nAtoms; i++){
135	gezelter	454
136			vx = atoms[i]->get_vx();
137			vy = atoms[i]->get_vy();
138			vz = atoms[i]->get_vz();
139
140	gezelter	457	atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
141			atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
142			atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
143	gezelter	453	}
144	gezelter	458	if( nOriented ){
145	gezelter	454
146	gezelter	458	for( i=0; i < nAtoms; i++ ){
147	gezelter	454
148			if( atoms[i]->isDirectional() ){
149
150			dAtom = (DirectionalAtom *)atoms[i];
151
152			jx = dAtom->getJx();
153			jy = dAtom->getJy();
154			jz = dAtom->getJz();
155
156			dAtom->setJx( jx * (1.0 - zetaScale));
157			dAtom->setJy( jy * (1.0 - zetaScale));
158			dAtom->setJz( jz * (1.0 - zetaScale));
159			}
160			}
161			}
162	gezelter	453	}
163
164	gezelter	457	void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
165	gezelter	453
166			int i;
167	gezelter	457	double r[3];
168			double boxNum[3];
169			double percentScale[3];
170			double rxi, ryi, rzi;
171	gezelter	453
172			// first determine the scaling factor from the box size change
173	gezelter	457	percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
174			percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
175			percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
176	gezelter	453
177			for (i=0; i < nMols; i++) {
178
179	gezelter	458	molecules[i].getCOM(r);
180	gezelter	453
181	gezelter	457	// find the minimum image coordinates of the molecular centers of mass:
182	gezelter	453
183	gezelter	457	boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
184			(double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
185	gezelter	453
186	gezelter	457	boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
187			(double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
188	gezelter	453
189	gezelter	457	boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
190			(double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
191	gezelter	453
192	gezelter	457	rxi = r[0] - boxNum[0];
193			ryi = r[1] - boxNum[1];
194			rzi = r[2] - boxNum[2];
195
196	gezelter	453	// update the minimum image coordinates using the scaling factor
197	gezelter	457	rxi += rxi*percentScale[0];
198			ryi += ryi*percentScale[1];
199			rzi += rzi*percentScale[2];
200	gezelter	453
201	gezelter	457	r[0] = rxi + boxNum[0];
202			r[1] = ryi + boxNum[1];
203			r[2] = rzi + boxNum[2];
204
205	gezelter	458	molecules[i].moveCOM(r);
206	gezelter	453	}
207			}