| 1 |
< |
/* |
| 2 |
< |
* Shapes_FF.cpp |
| 3 |
< |
* oopse |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
|
* |
| 4 |
< |
* Created by Chris Fennell on 10/20/04. |
| 5 |
< |
* Copyright 2004 __MyCompanyName__. All rights reserved. |
| 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 |
< |
|
| 41 |
> |
|
| 42 |
|
#include <stdlib.h> |
| 43 |
|
#include <stdio.h> |
| 44 |
|
#include <string.h> |
| 65 |
|
#include "UseTheForce/mpiForceField.h" |
| 66 |
|
#endif // is_mpi |
| 67 |
|
|
| 68 |
< |
using namespace std; |
| 68 |
> |
|
| 69 |
|
using namespace oopse; |
| 70 |
|
|
| 71 |
|
Shapes_FF::~Shapes_FF(){ |
| 85 |
|
void Shapes_FF::calcRcut( void ){ |
| 86 |
|
|
| 87 |
|
#ifdef IS_MPI |
| 88 |
< |
double tempShapesRcut = shapesRcut; |
| 88 |
> |
double tempShapesRcut = bigContact; |
| 89 |
|
MPI_Allreduce( &tempShapesRcut, &shapesRcut, 1, MPI_DOUBLE, MPI_MAX, |
| 90 |
|
MPI_COMM_WORLD); |
| 91 |
+ |
#else |
| 92 |
+ |
shapesRcut = bigContact; |
| 93 |
|
#endif //is_mpi |
| 94 |
|
entry_plug->setDefaultRcut(shapesRcut); |
| 95 |
|
} |
| 104 |
|
|
| 105 |
|
char readLine[1024]; |
| 106 |
|
|
| 107 |
< |
string fileName; |
| 108 |
< |
string shapeFileName; |
| 109 |
< |
string tempString; |
| 107 |
> |
std::string fileName; |
| 108 |
> |
std::string shapeFileName; |
| 109 |
> |
std::string tempString; |
| 110 |
|
|
| 111 |
|
char *nameToken; |
| 112 |
|
char *delim = " ,;\t\n"; |
| 116 |
|
int nStrength = 0; |
| 117 |
|
int myATID; |
| 118 |
|
int isError; |
| 119 |
< |
string nameString; |
| 119 |
> |
std::string nameString; |
| 120 |
|
AtomType* at; |
| 121 |
|
DirectionalAtomType* dat; |
| 122 |
|
ShapeAtomType* st; |
| 123 |
|
|
| 124 |
< |
map<string, AtomType*>::iterator iter; |
| 124 |
> |
std::map<string, AtomType*>::iterator iter; |
| 125 |
|
|
| 126 |
|
// vectors for shape transfer to fortran |
| 127 |
< |
vector<RealSphericalHarmonic*> tempSHVector; |
| 128 |
< |
vector<int> contactL; |
| 129 |
< |
vector<int> contactM; |
| 130 |
< |
vector<int> contactFunc; |
| 131 |
< |
vector<double> contactCoeff; |
| 132 |
< |
vector<int> rangeL; |
| 133 |
< |
vector<int> rangeM; |
| 134 |
< |
vector<int> rangeFunc; |
| 135 |
< |
vector<double> rangeCoeff; |
| 136 |
< |
vector<int> strengthL; |
| 137 |
< |
vector<int> strengthM; |
| 138 |
< |
vector<int> strengthFunc; |
| 139 |
< |
vector<double> strengthCoeff; |
| 127 |
> |
std::vector<RealSphericalHarmonic*> tempSHVector; |
| 128 |
> |
std::vector<int> contactL; |
| 129 |
> |
std::vector<int> contactM; |
| 130 |
> |
std::vector<int> contactFunc; |
| 131 |
> |
std::vector<double> contactCoeff; |
| 132 |
> |
std::vector<int> rangeL; |
| 133 |
> |
std::vector<int> rangeM; |
| 134 |
> |
std::vector<int> rangeFunc; |
| 135 |
> |
std::vector<double> rangeCoeff; |
| 136 |
> |
std::vector<int> strengthL; |
| 137 |
> |
std::vector<int> strengthM; |
| 138 |
> |
std::vector<int> strengthFunc; |
| 139 |
> |
std::vector<double> strengthCoeff; |
| 140 |
|
|
| 141 |
|
// generate the force file name |
| 142 |
|
fileName = "Shapes.frc"; |
| 204 |
|
st = new ShapeAtomType(); |
| 205 |
|
|
| 206 |
|
st->setName(nameString); |
| 207 |
< |
myATID = atomTypeMap.size(); |
| 207 |
> |
myATID = atomTypeMap.size() + 1; |
| 208 |
|
st->setIdent(myATID); |
| 209 |
|
parseShapeFile(shapeFileName, st); |
| 210 |
|
st->complete(); |
| 211 |
|
atomTypeMap.insert(make_pair(nameString, st)); |
| 212 |
|
|
| 213 |
|
} else { |
| 214 |
< |
// atomType map already contained this string (i.e. it was |
| 214 |
> |
// atomType map already contained this std::string (i.e. it was |
| 215 |
|
// declared in a previous block, and we just need to add |
| 216 |
|
// the shape-specific information for this AtomType: |
| 217 |
|
|
| 291 |
|
|
| 292 |
|
isError = 0; |
| 293 |
|
myATID = at->getIdent(); |
| 294 |
+ |
|
| 295 |
|
makeShape( &nContact, &contactL[0], &contactM[0], &contactFunc[0], |
| 296 |
|
&contactCoeff[0], |
| 297 |
|
&nRange, &rangeL[0], &rangeM[0], &rangeFunc[0], |
| 300 |
|
&strengthFunc[0], &strengthCoeff[0], |
| 301 |
|
&myATID, |
| 302 |
|
&isError); |
| 303 |
+ |
|
| 304 |
|
if( isError ){ |
| 305 |
|
sprintf( painCave.errMsg, |
| 306 |
|
"Error initializing the \"%s\" shape in fortran\n", |
| 312 |
|
} |
| 313 |
|
} |
| 314 |
|
|
| 315 |
+ |
isError = 0; |
| 316 |
+ |
completeShapeFF(&isError); |
| 317 |
+ |
if( isError ){ |
| 318 |
+ |
sprintf( painCave.errMsg, |
| 319 |
+ |
"Error completing Shape FF in fortran\n"); |
| 320 |
+ |
painCave.isFatal = 1; |
| 321 |
+ |
simError(); |
| 322 |
+ |
} |
| 323 |
+ |
|
| 324 |
|
#ifdef IS_MPI |
| 325 |
|
sprintf( checkPointMsg, |
| 326 |
|
"Shapes_FF atom structures successfully sent to fortran\n" ); |
| 336 |
|
void Shapes_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
| 337 |
|
|
| 338 |
|
int i,j,k; |
| 339 |
< |
map<string, AtomType*>::iterator iter; |
| 339 |
> |
std::map<string, AtomType*>::iterator iter; |
| 340 |
|
|
| 341 |
|
// initialize the atoms |
| 342 |
|
DirectionalAtom* dAtom; |
| 343 |
|
AtomType* at; |
| 344 |
|
DirectionalAtomType* dat; |
| 345 |
|
ShapeAtomType* sat; |
| 346 |
< |
double sigma; |
| 346 |
> |
double longCutoff; |
| 347 |
|
double ji[3]; |
| 348 |
|
double inertialMat[3][3]; |
| 349 |
|
Mat3x3d momInt; |
| 350 |
< |
string myTypeString; |
| 350 |
> |
std::string myTypeString; |
| 351 |
|
|
| 352 |
+ |
bigContact = 0.0; |
| 353 |
+ |
|
| 354 |
|
for( i=0; i<nAtoms; i++ ){ |
| 355 |
|
|
| 356 |
< |
myTypeString = the_atoms[i]->getType(); |
| 356 |
> |
myTypeString = the_atoms[i]->getType().c_str(); |
| 357 |
|
iter = atomTypeMap.find(myTypeString); |
| 358 |
|
|
| 359 |
|
if (iter == atomTypeMap.end()) { |
| 360 |
|
sprintf( painCave.errMsg, |
| 361 |
|
"AtomType error, %s not found in force file.\n", |
| 362 |
< |
the_atoms[i]->getType() ); |
| 362 |
> |
the_atoms[i]->getType().c_str() ); |
| 363 |
|
painCave.isFatal = 1; |
| 364 |
|
simError(); |
| 365 |
|
} else { |
| 372 |
|
if ( at->isShape() ) { |
| 373 |
|
|
| 374 |
|
sat = (ShapeAtomType*)at; |
| 375 |
< |
sigma = findLargestContactDistance(sat); |
| 376 |
< |
if (sigma > bigSigma) bigSigma = sigma; |
| 377 |
< |
|
| 375 |
> |
longCutoff = findCutoffDistance(sat); |
| 376 |
> |
if (longCutoff > bigContact) bigContact = longCutoff; |
| 377 |
> |
cout << bigContact << " is the cutoff value\n"; |
| 378 |
> |
|
| 379 |
> |
entry_plug->useShapes = 1; |
| 380 |
|
} |
| 381 |
|
|
| 382 |
|
the_atoms[i]->setHasCharge(at->isCharge()); |
| 449 |
|
int nTokens; |
| 450 |
|
Mat3x3d momInert; |
| 451 |
|
RealSphericalHarmonic* rsh; |
| 452 |
< |
vector<RealSphericalHarmonic*> functionVector; |
| 452 |
> |
std::vector<RealSphericalHarmonic*> functionVector; |
| 453 |
|
ifstrstream shapeFile; |
| 454 |
< |
string tempString; |
| 454 |
> |
std::string tempString; |
| 455 |
|
|
| 456 |
|
shapeFile.open( shapeFileName.c_str() ); |
| 457 |
|
|
| 499 |
|
painCave.severity = OOPSE_ERROR; |
| 500 |
|
painCave.isFatal = 1; |
| 501 |
|
simError(); |
| 502 |
< |
|
| 502 |
> |
} else { |
| 503 |
|
token = strtok(inLine, delim); |
| 504 |
|
token = strtok(NULL, delim); |
| 505 |
|
st->setMass(atof(token)); |
| 526 |
|
if( inLine[0] != '!' && inLine[0] != '#' ){ |
| 527 |
|
// end marks section completion |
| 528 |
|
if (isEndLine(inLine)) break; |
| 480 |
– |
|
| 529 |
|
nTokens = countTokens(inLine, delim); |
| 530 |
|
if (nTokens != 0) { |
| 531 |
|
if (nTokens < 4) { |
| 535 |
|
painCave.severity = OOPSE_ERROR; |
| 536 |
|
painCave.isFatal = 1; |
| 537 |
|
simError(); |
| 538 |
< |
|
| 538 |
> |
} else { |
| 539 |
|
// read in a spherical harmonic function |
| 540 |
|
token = strtok(inLine, delim); |
| 541 |
|
rsh = new RealSphericalHarmonic(); |
| 558 |
|
} |
| 559 |
|
|
| 560 |
|
// pass contact functions to ShapeType |
| 561 |
+ |
|
| 562 |
|
st->setContactFuncs(functionVector); |
| 563 |
|
|
| 564 |
|
// now grab the range functions |
| 581 |
|
painCave.severity = OOPSE_ERROR; |
| 582 |
|
painCave.isFatal = 1; |
| 583 |
|
simError(); |
| 584 |
+ |
} else { |
| 585 |
|
|
| 586 |
|
// read in a spherical harmonic function |
| 587 |
|
token = strtok(inLine, delim); |
| 628 |
|
painCave.severity = OOPSE_ERROR; |
| 629 |
|
painCave.isFatal = 1; |
| 630 |
|
simError(); |
| 631 |
+ |
} else { |
| 632 |
|
|
| 633 |
|
// read in a spherical harmonic function |
| 634 |
|
token = strtok(inLine, delim); |
| 662 |
|
int i, j, nSteps; |
| 663 |
|
double theta, thetaStep, thetaMin, costheta; |
| 664 |
|
double phi, phiStep; |
| 665 |
< |
double sigma, bigSigma; |
| 665 |
> |
double sigma, bs; |
| 666 |
> |
|
| 667 |
> |
nSteps = 16; |
| 668 |
> |
|
| 669 |
> |
thetaStep = M_PI / nSteps; |
| 670 |
> |
thetaMin = thetaStep / 2.0; |
| 671 |
> |
phiStep = thetaStep * 2.0; |
| 672 |
> |
bs = 0.0; |
| 673 |
> |
|
| 674 |
> |
for (i = 0; i < nSteps; i++) { |
| 675 |
> |
|
| 676 |
> |
theta = thetaMin + i * thetaStep; |
| 677 |
> |
costheta = cos(theta); |
| 678 |
|
|
| 679 |
+ |
for (j = 0; j < nSteps; j++) { |
| 680 |
+ |
|
| 681 |
+ |
phi = j*phiStep; |
| 682 |
+ |
|
| 683 |
+ |
sigma = st->getContactValueAt(costheta, phi); |
| 684 |
+ |
|
| 685 |
+ |
if (sigma > bs) bs = sigma; |
| 686 |
+ |
} |
| 687 |
+ |
} |
| 688 |
+ |
|
| 689 |
+ |
return bs; |
| 690 |
+ |
} |
| 691 |
+ |
|
| 692 |
+ |
|
| 693 |
+ |
double Shapes_FF::findCutoffDistance(ShapeAtomType* st) { |
| 694 |
+ |
int i, j, nSteps; |
| 695 |
+ |
double theta, thetaStep, thetaMin, costheta; |
| 696 |
+ |
double phi, phiStep; |
| 697 |
+ |
double sigma, range; |
| 698 |
+ |
double bigCut, tempCut; |
| 699 |
+ |
|
| 700 |
|
nSteps = 16; |
| 701 |
|
|
| 702 |
|
thetaStep = M_PI / nSteps; |
| 703 |
|
thetaMin = thetaStep / 2.0; |
| 704 |
|
phiStep = thetaStep * 2.0; |
| 705 |
< |
bigSigma = 0.0; |
| 705 |
> |
bigCut = 0.0; |
| 706 |
|
|
| 707 |
|
for (i = 0; i < nSteps; i++) { |
| 708 |
|
|
| 714 |
|
phi = j*phiStep; |
| 715 |
|
|
| 716 |
|
sigma = st->getContactValueAt(costheta, phi); |
| 717 |
< |
|
| 718 |
< |
if (sigma > bigSigma) bigSigma = sigma; |
| 717 |
> |
range = st->getRangeValueAt(costheta, phi); |
| 718 |
> |
|
| 719 |
> |
// cutoff for a shape is taken to be (2.5*rangeVal + contactVal) |
| 720 |
> |
tempCut = 1.5*range + sigma; |
| 721 |
> |
|
| 722 |
> |
if (tempCut > bigCut) bigCut = tempCut; |
| 723 |
|
} |
| 724 |
|
} |
| 725 |
< |
|
| 726 |
< |
return bigSigma; |
| 725 |
> |
|
| 726 |
> |
return bigCut; |
| 727 |
|
} |
