src/integrators/NPT.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include <math.h>

#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/NPT.hpp"
#include "math/SquareMatrix3.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/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.

namespace oopse {

  NPT::NPT(SimInfo* info) :
    VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) {

      Globals* simParams = info_->getSimParams();
    
      if (!simParams->getUseIntialExtendedSystemState()) {
        Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
        currSnapshot->setChi(0.0);
        currSnapshot->setIntegralOfChiDt(0.0);
        currSnapshot->setEta(Mat3x3d(0.0));
      }
    
      if (!simParams->haveTargetTemp()) {
        sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n");
        painCave.isFatal = 1;
        painCave.severity = OOPSE_ERROR;
        simError();
      } else {
        targetTemp = simParams->getTargetTemp();
      }

      // We must set tauThermostat
      if (!simParams->haveTauThermostat()) {
        sprintf(painCave.errMsg, "If you use the constant temperature\n"
                "\tintegrator, you must set tauThermostat_.\n");

        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
      } else {
        tauThermostat = simParams->getTauThermostat();
      }

      if (!simParams->haveTargetPressure()) {
        sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
                "   without a targetPressure!\n");

        painCave.isFatal = 1;
        simError();
      } else {
        targetPressure = simParams->getTargetPressure();
      }
    
      if (!simParams->haveTauBarostat()) {
        sprintf(painCave.errMsg,
                "If you use the NPT integrator, you must set tauBarostat.\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
      } else {
        tauBarostat = simParams->getTauBarostat();
      }
    
      tt2 = tauThermostat * tauThermostat;
      tb2 = tauBarostat * tauBarostat;

      update();
    }

  NPT::~NPT() {
  }

  void NPT::doUpdate() {

    oldPos.resize(info_->getNIntegrableObjects());
    oldVel.resize(info_->getNIntegrableObjects());
    oldJi.resize(info_->getNIntegrableObjects());

  }

  void NPT::moveA() {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d Tb, ji;
    RealType mass;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Vector3d sc;
    int index;

    chi= currentSnapshot_->getChi();
    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    loadEta();
    
    instaTemp =thermo.getTemperature();
    press = thermo.getPressureTensor();
    instaPress = OOPSEConstant::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
    instaVol =thermo.getVolume();

    Vector3d  COM = info_->getCom();

    //evolve velocity half step

    calcVelScale();

    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {
                
        vel = integrableObject->getVel();
        frc = integrableObject->getFrc();

        mass = integrableObject->getMass();

        getVelScaleA(sc, vel);

        // velocity half step  (use chi from previous step here):
        //vel[j] += dt2 * ((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]);
        vel += dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc;
        integrableObject->setVel(vel);

        if (integrableObject->isDirectional()) {

          // get and convert the torque to body frame

          Tb = integrableObject->lab2Body(integrableObject->getTrq());

          // get the angular momentum, and propagate a half step

          ji = integrableObject->getJ();

          //ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
          ji += dt2*OOPSEConstant::energyConvert * Tb - dt2*chi* ji;
                
          rotAlgo->rotate(integrableObject, ji, dt);

          integrableObject->setJ(ji);
        }
            
      }
    }
    // evolve chi and eta  half step

    chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
    
    evolveEtaA();

    //calculate the integral of chidt
    integralOfChidt += dt2 * chi;
    
    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {
        oldPos[index++] = integrableObject->getPos();            
      }
    }
    
    //the first estimation of r(t+dt) is equal to  r(t)

    for(int k = 0; k < maxIterNum_; k++) {
      index = 0;
      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
             integrableObject = mol->nextIntegrableObject(j)) {

          vel = integrableObject->getVel();
          pos = integrableObject->getPos();

          this->getPosScale(pos, COM, index, sc);

          pos = oldPos[index] + dt * (vel + sc);
          integrableObject->setPos(pos);     

          ++index;
        }
      }

      rattle->constraintA();
    }

    // Scale the box after all the positions have been moved:

    this->scaleSimBox();

    currentSnapshot_->setChi(chi);
    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);

    saveEta();
  }

  void NPT::moveB(void) {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    int index;
    Vector3d Tb;
    Vector3d ji;
    Vector3d sc;
    Vector3d vel;
    Vector3d frc;
    RealType mass;


    chi= currentSnapshot_->getChi();
    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    RealType oldChi  = chi;
    RealType prevChi;

    loadEta();
    
    //save velocity and angular momentum
    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {
                
        oldVel[index] = integrableObject->getVel();
        oldJi[index] = integrableObject->getJ();
        ++index;
      }
    }

    // do the iteration:
    instaVol =thermo.getVolume();

    for(int k = 0; k < maxIterNum_; k++) {
      instaTemp =thermo.getTemperature();
      instaPress =thermo.getPressure();

      // evolve chi another half step using the temperature at t + dt/2
      prevChi = chi;
      chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;

      //evolve eta
      this->evolveEtaB();
      this->calcVelScale();

      index = 0;
      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
             integrableObject = mol->nextIntegrableObject(j)) {            

          frc = integrableObject->getFrc();
          vel = integrableObject->getVel();

          mass = integrableObject->getMass();

          getVelScaleB(sc, index);

          // velocity half step
          //vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]);
          vel = oldVel[index] + dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc;
          integrableObject->setVel(vel);

          if (integrableObject->isDirectional()) {
            // get and convert the torque to body frame
            Tb = integrableObject->lab2Body(integrableObject->getTrq());

            //ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi[3*i+j]*chi);
            ji = oldJi[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi*oldJi[index];
            integrableObject->setJ(ji);
          }

          ++index;
        }
      }
        
      rattle->constraintB();

      if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
        break;
    }

    //calculate integral of chidt
    integralOfChidt += dt2 * chi;

    currentSnapshot_->setChi(chi);
    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);    

    saveEta();
  }

  void NPT::resetIntegrator(){
      currentSnapshot_->setChi(0.0);
      currentSnapshot_->setIntegralOfChiDt(0.0);
      resetEta();
  }


    void NPT::resetEta() {
      Mat3x3d etaMat(0.0);
      currentSnapshot_->setEta(etaMat);    
    }
    
}
Revision:	963
Committed:	Wed May 17 21:51:42 2006 UTC (18 years, 11 months ago) by tim
Original Path:	*trunk/src/integrators/NPT.cpp*
File size:	10716 byte(s)
Log Message:	Adding single precision capabilities to c++ side
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	gezelter	2	#include <math.h>
43
44	tim	3	#include "brains/SimInfo.hpp"
45			#include "brains/Thermo.hpp"
46	gezelter	246	#include "integrators/NPT.hpp"
47			#include "math/SquareMatrix3.hpp"
48			#include "primitives/Molecule.hpp"
49			#include "utils/OOPSEConstant.hpp"
50	tim	3	#include "utils/simError.h"
51	gezelter	2
52			// Basic isotropic thermostating and barostating via the Melchionna
53			// modification of the Hoover algorithm:
54			//
55			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
56			// Molec. Phys., 78, 533.
57			//
58			// and
59			//
60			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
61
62	gezelter	246	namespace oopse {
63	gezelter	2
64	gezelter	507	NPT::NPT(SimInfo* info) :
65	gezelter	246	VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) {
66	gezelter	2
67	gezelter	507	Globals* simParams = info_->getSimParams();
68	gezelter	246
69	tim	665	if (!simParams->getUseIntialExtendedSystemState()) {
70	gezelter	246	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
71			currSnapshot->setChi(0.0);
72			currSnapshot->setIntegralOfChiDt(0.0);
73			currSnapshot->setEta(Mat3x3d(0.0));
74	gezelter	507	}
75	gezelter	246
76	gezelter	507	if (!simParams->haveTargetTemp()) {
77	gezelter	246	sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n");
78			painCave.isFatal = 1;
79			painCave.severity = OOPSE_ERROR;
80			simError();
81	gezelter	507	} else {
82	gezelter	246	targetTemp = simParams->getTargetTemp();
83	gezelter	507	}
84	gezelter	2
85	gezelter	507	// We must set tauThermostat
86			if (!simParams->haveTauThermostat()) {
87	gezelter	246	sprintf(painCave.errMsg, "If you use the constant temperature\n"
88	gezelter	507	"\tintegrator, you must set tauThermostat_.\n");
89	gezelter	2
90	gezelter	246	painCave.severity = OOPSE_ERROR;
91			painCave.isFatal = 1;
92			simError();
93	gezelter	507	} else {
94	gezelter	246	tauThermostat = simParams->getTauThermostat();
95	gezelter	507	}
96	gezelter	2
97	gezelter	507	if (!simParams->haveTargetPressure()) {
98	gezelter	246	sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
99	gezelter	507	" without a targetPressure!\n");
100	gezelter	2
101	gezelter	246	painCave.isFatal = 1;
102			simError();
103	gezelter	507	} else {
104	gezelter	246	targetPressure = simParams->getTargetPressure();
105	gezelter	507	}
106	gezelter	246
107	gezelter	507	if (!simParams->haveTauBarostat()) {
108	gezelter	246	sprintf(painCave.errMsg,
109			"If you use the NPT integrator, you must set tauBarostat.\n");
110			painCave.severity = OOPSE_ERROR;
111			painCave.isFatal = 1;
112			simError();
113	gezelter	507	} else {
114	gezelter	246	tauBarostat = simParams->getTauBarostat();
115	gezelter	507	}
116	gezelter	246
117	gezelter	507	tt2 = tauThermostat * tauThermostat;
118			tb2 = tauBarostat * tauBarostat;
119	gezelter	2
120	gezelter	507	update();
121			}
122	gezelter	2
123	gezelter	507	NPT::~NPT() {
124			}
125	gezelter	2
126	gezelter	507	void NPT::doUpdate() {
127	gezelter	2
128	gezelter	246	oldPos.resize(info_->getNIntegrableObjects());
129			oldVel.resize(info_->getNIntegrableObjects());
130			oldJi.resize(info_->getNIntegrableObjects());
131	gezelter	2
132	gezelter	507	}
133	gezelter	2
134	gezelter	507	void NPT::moveA() {
135	gezelter	246	SimInfo::MoleculeIterator i;
136			Molecule::IntegrableObjectIterator j;
137			Molecule* mol;
138			StuntDouble* integrableObject;
139			Vector3d Tb, ji;
140	tim	963	RealType mass;
141	gezelter	246	Vector3d vel;
142			Vector3d pos;
143			Vector3d frc;
144			Vector3d sc;
145			int index;
146	gezelter	2
147	gezelter	246	chi= currentSnapshot_->getChi();
148			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
149			loadEta();
150
151			instaTemp =thermo.getTemperature();
152			press = thermo.getPressureTensor();
153			instaPress = OOPSEConstant::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
154			instaVol =thermo.getVolume();
155	gezelter	2
156	gezelter	246	Vector3d COM = info_->getCom();
157	gezelter	2
158	gezelter	246	//evolve velocity half step
159	gezelter	2
160	gezelter	246	calcVelScale();
161	gezelter	2
162	gezelter	246	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
163	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
164			integrableObject = mol->nextIntegrableObject(j)) {
165	gezelter	246
166	gezelter	507	vel = integrableObject->getVel();
167			frc = integrableObject->getFrc();
168	gezelter	2
169	gezelter	507	mass = integrableObject->getMass();
170	gezelter	2
171	gezelter	507	getVelScaleA(sc, vel);
172	gezelter	2
173	gezelter	507	// velocity half step (use chi from previous step here):
174			//vel[j] += dt2 * ((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]);
175			vel += dt2OOPSEConstant::energyConvert/mass frc - dt2*sc;
176			integrableObject->setVel(vel);
177	gezelter	2
178	gezelter	507	if (integrableObject->isDirectional()) {
179	gezelter	2
180	gezelter	507	// get and convert the torque to body frame
181	gezelter	2
182	gezelter	507	Tb = integrableObject->lab2Body(integrableObject->getTrq());
183	gezelter	2
184	gezelter	507	// get the angular momentum, and propagate a half step
185	gezelter	2
186	gezelter	507	ji = integrableObject->getJ();
187	gezelter	2
188	gezelter	507	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
189			ji += dt2OOPSEConstant::energyConvert Tb - dt2chi ji;
190	gezelter	246
191	gezelter	507	rotAlgo->rotate(integrableObject, ji, dt);
192	gezelter	2
193	gezelter	507	integrableObject->setJ(ji);
194			}
195	gezelter	246
196	gezelter	507	}
197	gezelter	246	}
198			// evolve chi and eta half step
199	gezelter	2
200	gezelter	246	chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
201
202			evolveEtaA();
203	gezelter	2
204	gezelter	246	//calculate the integral of chidt
205			integralOfChidt += dt2 * chi;
206
207			index = 0;
208			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
209	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
210			integrableObject = mol->nextIntegrableObject(j)) {
211			oldPos[index++] = integrableObject->getPos();
212			}
213	gezelter	2	}
214	gezelter	246
215			//the first estimation of r(t+dt) is equal to r(t)
216	gezelter	2
217	gezelter	246	for(int k = 0; k < maxIterNum_; k++) {
218	gezelter	507	index = 0;
219			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
220			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
221			integrableObject = mol->nextIntegrableObject(j)) {
222	gezelter	2
223	gezelter	507	vel = integrableObject->getVel();
224			pos = integrableObject->getPos();
225	gezelter	2
226	gezelter	507	this->getPosScale(pos, COM, index, sc);
227	gezelter	2
228	gezelter	507	pos = oldPos[index] + dt * (vel + sc);
229			integrableObject->setPos(pos);
230	gezelter	2
231	gezelter	507	++index;
232			}
233			}
234	gezelter	2
235	gezelter	507	rattle->constraintA();
236	gezelter	246	}
237	gezelter	2
238	gezelter	246	// Scale the box after all the positions have been moved:
239	gezelter	2
240	gezelter	246	this->scaleSimBox();
241	gezelter	2
242	gezelter	246	currentSnapshot_->setChi(chi);
243			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
244	gezelter	2
245	gezelter	246	saveEta();
246	gezelter	507	}
247	gezelter	2
248	gezelter	507	void NPT::moveB(void) {
249	gezelter	246	SimInfo::MoleculeIterator i;
250			Molecule::IntegrableObjectIterator j;
251			Molecule* mol;
252			StuntDouble* integrableObject;
253			int index;
254			Vector3d Tb;
255			Vector3d ji;
256			Vector3d sc;
257			Vector3d vel;
258			Vector3d frc;
259	tim	963	RealType mass;
260	gezelter	2
261
262	gezelter	246	chi= currentSnapshot_->getChi();
263			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
264	tim	963	RealType oldChi = chi;
265			RealType prevChi;
266	gezelter	2
267	gezelter	246	loadEta();
268
269			//save velocity and angular momentum
270			index = 0;
271			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
272	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
273			integrableObject = mol->nextIntegrableObject(j)) {
274	gezelter	246
275	gezelter	507	oldVel[index] = integrableObject->getVel();
276			oldJi[index] = integrableObject->getJ();
277			++index;
278			}
279	gezelter	2	}
280
281	gezelter	246	// do the iteration:
282			instaVol =thermo.getVolume();
283	gezelter	2
284	gezelter	246	for(int k = 0; k < maxIterNum_; k++) {
285	gezelter	507	instaTemp =thermo.getTemperature();
286			instaPress =thermo.getPressure();
287	gezelter	2
288	gezelter	507	// evolve chi another half step using the temperature at t + dt/2
289			prevChi = chi;
290			chi = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;
291	gezelter	2
292	gezelter	507	//evolve eta
293			this->evolveEtaB();
294			this->calcVelScale();
295	gezelter	2
296	gezelter	507	index = 0;
297			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
298			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
299			integrableObject = mol->nextIntegrableObject(j)) {
300	gezelter	2
301	gezelter	507	frc = integrableObject->getFrc();
302			vel = integrableObject->getVel();
303	gezelter	2
304	gezelter	507	mass = integrableObject->getMass();
305	gezelter	2
306	gezelter	507	getVelScaleB(sc, index);
307	gezelter	2
308	gezelter	507	// velocity half step
309			//vel[j] = oldVel[3 * i + j] + dt2 ((frc[j] / mass) OOPSEConstant::energyConvert - sc[j]);
310			vel = oldVel[index] + dt2OOPSEConstant::energyConvert/mass frc - dt2*sc;
311			integrableObject->setVel(vel);
312	gezelter	2
313	gezelter	507	if (integrableObject->isDirectional()) {
314			// get and convert the torque to body frame
315			Tb = integrableObject->lab2Body(integrableObject->getTrq());
316	gezelter	2
317	gezelter	507	//ji[j] = oldJi[3i + j] + dt2 (Tb[j] * OOPSEConstant::energyConvert - oldJi[3i+j]chi);
318			ji = oldJi[index] + dt2OOPSEConstant::energyConvertTb - dt2chioldJi[index];
319			integrableObject->setJ(ji);
320			}
321	gezelter	2
322	gezelter	507	++index;
323			}
324			}
325	gezelter	246
326	gezelter	507	rattle->constraintB();
327	gezelter	2
328	gezelter	507	if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
329			break;
330	gezelter	2	}
331
332	gezelter	246	//calculate integral of chidt
333			integralOfChidt += dt2 * chi;
334	gezelter	2
335	gezelter	246	currentSnapshot_->setChi(chi);
336			currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
337	gezelter	2
338	gezelter	246	saveEta();
339	gezelter	507	}
340	gezelter	2
341	tim	546	void NPT::resetIntegrator(){
342			currentSnapshot_->setChi(0.0);
343			currentSnapshot_->setIntegralOfChiDt(0.0);
344			resetEta();
345			}
346
347
348			void NPT::resetEta() {
349			Mat3x3d etaMat(0.0);
350			currentSnapshot_->setEta(etaMat);
351			}
352
353	gezelter	2	}