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:	1277
Committed:	Mon Jul 14 12:35:58 2008 UTC (16 years, 9 months ago) by gezelter
File size:	10715 byte(s)
Log Message:	Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
#	Content
1	/*
2	* 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	#include <math.h>
43
44	#include "brains/SimInfo.hpp"
45	#include "brains/Thermo.hpp"
46	#include "integrators/NPT.hpp"
47	#include "math/SquareMatrix3.hpp"
48	#include "primitives/Molecule.hpp"
49	#include "utils/OOPSEConstant.hpp"
50	#include "utils/simError.h"
51
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	namespace oopse {
63
64	NPT::NPT(SimInfo* info) :
65	VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) {
66
67	Globals* simParams = info_->getSimParams();
68
69	if (!simParams->getUseIntialExtendedSystemState()) {
70	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
71	currSnapshot->setChi(0.0);
72	currSnapshot->setIntegralOfChiDt(0.0);
73	currSnapshot->setEta(Mat3x3d(0.0));
74	}
75
76	if (!simParams->haveTargetTemp()) {
77	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	} else {
82	targetTemp = simParams->getTargetTemp();
83	}
84
85	// We must set tauThermostat
86	if (!simParams->haveTauThermostat()) {
87	sprintf(painCave.errMsg, "If you use the constant temperature\n"
88	"\tintegrator, you must set tauThermostat.\n");
89
90	painCave.severity = OOPSE_ERROR;
91	painCave.isFatal = 1;
92	simError();
93	} else {
94	tauThermostat = simParams->getTauThermostat();
95	}
96
97	if (!simParams->haveTargetPressure()) {
98	sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
99	" without a targetPressure!\n");
100
101	painCave.isFatal = 1;
102	simError();
103	} else {
104	targetPressure = simParams->getTargetPressure();
105	}
106
107	if (!simParams->haveTauBarostat()) {
108	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	} else {
114	tauBarostat = simParams->getTauBarostat();
115	}
116
117	tt2 = tauThermostat * tauThermostat;
118	tb2 = tauBarostat * tauBarostat;
119
120	update();
121	}
122
123	NPT::~NPT() {
124	}
125
126	void NPT::doUpdate() {
127
128	oldPos.resize(info_->getNIntegrableObjects());
129	oldVel.resize(info_->getNIntegrableObjects());
130	oldJi.resize(info_->getNIntegrableObjects());
131
132	}
133
134	void NPT::moveA() {
135	SimInfo::MoleculeIterator i;
136	Molecule::IntegrableObjectIterator j;
137	Molecule* mol;
138	StuntDouble* integrableObject;
139	Vector3d Tb, ji;
140	RealType mass;
141	Vector3d vel;
142	Vector3d pos;
143	Vector3d frc;
144	Vector3d sc;
145	int index;
146
147	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
156	Vector3d COM = info_->getCom();
157
158	//evolve velocity half step
159
160	calcVelScale();
161
162	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
163	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
164	integrableObject = mol->nextIntegrableObject(j)) {
165
166	vel = integrableObject->getVel();
167	frc = integrableObject->getFrc();
168
169	mass = integrableObject->getMass();
170
171	getVelScaleA(sc, vel);
172
173	// 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
178	if (integrableObject->isDirectional()) {
179
180	// get and convert the torque to body frame
181
182	Tb = integrableObject->lab2Body(integrableObject->getTrq());
183
184	// get the angular momentum, and propagate a half step
185
186	ji = integrableObject->getJ();
187
188	//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi);
189	ji += dt2OOPSEConstant::energyConvert Tb - dt2chi ji;
190
191	rotAlgo->rotate(integrableObject, ji, dt);
192
193	integrableObject->setJ(ji);
194	}
195
196	}
197	}
198	// evolve chi and eta half step
199
200	chi += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
201
202	evolveEtaA();
203
204	//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	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
210	integrableObject = mol->nextIntegrableObject(j)) {
211	oldPos[index++] = integrableObject->getPos();
212	}
213	}
214
215	//the first estimation of r(t+dt) is equal to r(t)
216
217	for(int k = 0; k < maxIterNum_; k++) {
218	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
223	vel = integrableObject->getVel();
224	pos = integrableObject->getPos();
225
226	this->getPosScale(pos, COM, index, sc);
227
228	pos = oldPos[index] + dt * (vel + sc);
229	integrableObject->setPos(pos);
230
231	++index;
232	}
233	}
234
235	rattle->constraintA();
236	}
237
238	// Scale the box after all the positions have been moved:
239
240	this->scaleSimBox();
241
242	currentSnapshot_->setChi(chi);
243	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
244
245	saveEta();
246	}
247
248	void NPT::moveB(void) {
249	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	RealType mass;
260
261
262	chi= currentSnapshot_->getChi();
263	integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
264	RealType oldChi = chi;
265	RealType prevChi;
266
267	loadEta();
268
269	//save velocity and angular momentum
270	index = 0;
271	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
272	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
273	integrableObject = mol->nextIntegrableObject(j)) {
274
275	oldVel[index] = integrableObject->getVel();
276	oldJi[index] = integrableObject->getJ();
277	++index;
278	}
279	}
280
281	// do the iteration:
282	instaVol =thermo.getVolume();
283
284	for(int k = 0; k < maxIterNum_; k++) {
285	instaTemp =thermo.getTemperature();
286	instaPress =thermo.getPressure();
287
288	// 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
292	//evolve eta
293	this->evolveEtaB();
294	this->calcVelScale();
295
296	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
301	frc = integrableObject->getFrc();
302	vel = integrableObject->getVel();
303
304	mass = integrableObject->getMass();
305
306	getVelScaleB(sc, index);
307
308	// 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
313	if (integrableObject->isDirectional()) {
314	// get and convert the torque to body frame
315	Tb = integrableObject->lab2Body(integrableObject->getTrq());
316
317	//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
322	++index;
323	}
324	}
325
326	rattle->constraintB();
327
328	if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged())
329	break;
330	}
331
332	//calculate integral of chidt
333	integralOfChidt += dt2 * chi;
334
335	currentSnapshot_->setChi(chi);
336	currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
337
338	saveEta();
339	}
340
341	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	}