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#include <cstdlib> |
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#include <cstring> |
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#include <cmath> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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#include <iostream> |
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using namespace std; |
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#include "fortranWrappers.hpp" |
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#include "MatVec3.h" |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
23 |
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} |
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|
25 |
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inline double min( double a, double b ){ |
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return (a < b ) ? a : b; |
27 |
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} |
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|
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SimInfo* currentInfo; |
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SimInfo::SimInfo(){ |
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excludes = NULL; |
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|
33 |
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n_constraints = 0; |
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nZconstraints = 0; |
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n_oriented = 0; |
42 |
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thermalTime = 0.0; |
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currentTime = 0.0; |
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rCut = 0.0; |
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origRcut = -1.0; |
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ecr = 0.0; |
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origEcr = -1.0; |
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est = 0.0; |
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oldEcr = 0.0; |
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oldRcut = 0.0; |
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|
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haveOrigRcut = 0; |
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haveOrigEcr = 0; |
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haveRcut = 0; |
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haveEcr = 0; |
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boxIsInit = 0; |
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resetTime = 1e99; |
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orthoRhombic = 0; |
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orthoTolerance = 1E-6; |
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useInitXSstate = true; |
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|
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usePBC = 0; |
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useLJ = 0; |
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useSticky = 0; |
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useDipole = 0; |
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useCharges = 0; |
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useDipoles = 0; |
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useReactionField = 0; |
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useGB = 0; |
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useEAM = 0; |
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|
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excludes = Exclude::Instance(); |
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|
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myConfiguration = new SimState(); |
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has_minimizer = false; |
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the_minimizer =NULL; |
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|
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wrapMeSimInfo( this ); |
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} |
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void SimInfo::setBoxM( double theBox[3][3] ){ |
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int i, j, status; |
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double smallestBoxL, maxCutoff; |
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int i, j; |
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double FortranHmat[9]; // to preserve compatibility with Fortran the |
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// ordering in the array is as follows: |
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// [ 0 3 6 ] |
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// [ 2 5 8 ] |
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double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
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|
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if( !boxIsInit ) boxIsInit = 1; |
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for(i=0; i < 3; i++) |
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void SimInfo::calcHmatInv( void ) { |
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int oldOrtho; |
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int i,j; |
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double smallDiag; |
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double tol; |
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invertMat3( Hmat, HmatInv ); |
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// Check the inverse to make sure it is sane: |
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|
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matMul3( Hmat, HmatInv, sanity ); |
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|
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// check to see if Hmat is orthorhombic |
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smallDiag = Hmat[0][0]; |
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if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
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if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
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tol = smallDiag * 1E-6; |
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oldOrtho = orthoRhombic; |
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|
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smallDiag = fabs(Hmat[0][0]); |
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if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
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if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
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tol = smallDiag * orthoTolerance; |
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|
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orthoRhombic = 1; |
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|
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for (i = 0; i < 3; i++ ) { |
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for (j = 0 ; j < 3; j++) { |
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if (i != j) { |
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if (orthoRhombic) { |
181 |
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if (Hmat[i][j] >= tol) orthoRhombic = 0; |
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if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
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} |
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} |
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} |
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} |
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} |
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double SimInfo::matDet3(double a[3][3]) { |
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int i, j, k; |
189 |
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double determinant; |
190 |
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|
191 |
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determinant = 0.0; |
192 |
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|
193 |
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for(i = 0; i < 3; i++) { |
194 |
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j = (i+1)%3; |
195 |
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k = (i+2)%3; |
196 |
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|
197 |
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determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
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} |
192 |
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|
193 |
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return determinant; |
194 |
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} |
195 |
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|
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void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
197 |
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|
198 |
< |
int i, j, k, l, m, n; |
199 |
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double determinant; |
200 |
< |
|
201 |
< |
determinant = matDet3( a ); |
202 |
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|
203 |
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if (determinant == 0.0) { |
204 |
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sprintf( painCave.errMsg, |
205 |
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"Can't invert a matrix with a zero determinant!\n"); |
206 |
< |
painCave.isFatal = 1; |
207 |
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simError(); |
208 |
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} |
209 |
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|
210 |
< |
for (i=0; i < 3; i++) { |
211 |
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j = (i+1)%3; |
212 |
< |
k = (i+2)%3; |
213 |
< |
for(l = 0; l < 3; l++) { |
214 |
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m = (l+1)%3; |
215 |
< |
n = (l+2)%3; |
216 |
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|
217 |
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b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
187 |
> |
if( oldOrtho != orthoRhombic ){ |
188 |
> |
|
189 |
> |
if( orthoRhombic ){ |
190 |
> |
sprintf( painCave.errMsg, |
191 |
> |
"OOPSE is switching from the default Non-Orthorhombic\n" |
192 |
> |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
193 |
> |
"\tThis is usually a good thing, but if you wan't the\n" |
194 |
> |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
195 |
> |
"\tvariable ( currently set to %G ) smaller.\n", |
196 |
> |
orthoTolerance); |
197 |
> |
simError(); |
198 |
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} |
199 |
< |
} |
200 |
< |
} |
201 |
< |
|
202 |
< |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
203 |
< |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
204 |
< |
|
205 |
< |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
206 |
< |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
207 |
< |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
208 |
< |
|
229 |
< |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
230 |
< |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
231 |
< |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
232 |
< |
|
233 |
< |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
234 |
< |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
235 |
< |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
236 |
< |
|
237 |
< |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
238 |
< |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
239 |
< |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
240 |
< |
} |
241 |
< |
|
242 |
< |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
243 |
< |
double a0, a1, a2; |
244 |
< |
|
245 |
< |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
246 |
< |
|
247 |
< |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
248 |
< |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
249 |
< |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
250 |
< |
} |
251 |
< |
|
252 |
< |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
253 |
< |
double temp[3][3]; |
254 |
< |
int i, j; |
255 |
< |
|
256 |
< |
for (i = 0; i < 3; i++) { |
257 |
< |
for (j = 0; j < 3; j++) { |
258 |
< |
temp[j][i] = in[i][j]; |
199 |
> |
else { |
200 |
> |
sprintf( painCave.errMsg, |
201 |
> |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
202 |
> |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
203 |
> |
"\tThis is usually because the box has deformed under\n" |
204 |
> |
"\tNPTf integration. If you wan't to live on the edge with\n" |
205 |
> |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
206 |
> |
"\tvariable ( currently set to %G ) larger.\n", |
207 |
> |
orthoTolerance); |
208 |
> |
simError(); |
209 |
|
} |
210 |
|
} |
261 |
– |
for (i = 0; i < 3; i++) { |
262 |
– |
for (j = 0; j < 3; j++) { |
263 |
– |
out[i][j] = temp[i][j]; |
264 |
– |
} |
265 |
– |
} |
211 |
|
} |
267 |
– |
|
268 |
– |
void SimInfo::printMat3(double A[3][3] ){ |
212 |
|
|
270 |
– |
std::cerr |
271 |
– |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
272 |
– |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
273 |
– |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
274 |
– |
} |
275 |
– |
|
276 |
– |
void SimInfo::printMat9(double A[9] ){ |
277 |
– |
|
278 |
– |
std::cerr |
279 |
– |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
280 |
– |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
281 |
– |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
282 |
– |
} |
283 |
– |
|
213 |
|
void SimInfo::calcBoxL( void ){ |
214 |
|
|
215 |
|
double dx, dy, dz, dsq; |
287 |
– |
int i; |
216 |
|
|
217 |
|
// boxVol = Determinant of Hmat |
218 |
|
|
223 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
224 |
|
dsq = dx*dx + dy*dy + dz*dz; |
225 |
|
boxL[0] = sqrt( dsq ); |
226 |
< |
maxCutoff = 0.5 * boxL[0]; |
226 |
> |
//maxCutoff = 0.5 * boxL[0]; |
227 |
|
|
228 |
|
// boxLy |
229 |
|
|
230 |
|
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
231 |
|
dsq = dx*dx + dy*dy + dz*dz; |
232 |
|
boxL[1] = sqrt( dsq ); |
233 |
< |
if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
233 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
234 |
|
|
235 |
+ |
|
236 |
|
// boxLz |
237 |
|
|
238 |
|
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
239 |
|
dsq = dx*dx + dy*dy + dz*dz; |
240 |
|
boxL[2] = sqrt( dsq ); |
241 |
< |
if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
241 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
242 |
> |
|
243 |
> |
//calculate the max cutoff |
244 |
> |
maxCutoff = calcMaxCutOff(); |
245 |
|
|
246 |
|
checkCutOffs(); |
247 |
|
|
248 |
|
} |
249 |
|
|
250 |
|
|
251 |
+ |
double SimInfo::calcMaxCutOff(){ |
252 |
+ |
|
253 |
+ |
double ri[3], rj[3], rk[3]; |
254 |
+ |
double rij[3], rjk[3], rki[3]; |
255 |
+ |
double minDist; |
256 |
+ |
|
257 |
+ |
ri[0] = Hmat[0][0]; |
258 |
+ |
ri[1] = Hmat[1][0]; |
259 |
+ |
ri[2] = Hmat[2][0]; |
260 |
+ |
|
261 |
+ |
rj[0] = Hmat[0][1]; |
262 |
+ |
rj[1] = Hmat[1][1]; |
263 |
+ |
rj[2] = Hmat[2][1]; |
264 |
+ |
|
265 |
+ |
rk[0] = Hmat[0][2]; |
266 |
+ |
rk[1] = Hmat[1][2]; |
267 |
+ |
rk[2] = Hmat[2][2]; |
268 |
+ |
|
269 |
+ |
crossProduct3(ri, rj, rij); |
270 |
+ |
distXY = dotProduct3(rk,rij) / norm3(rij); |
271 |
+ |
|
272 |
+ |
crossProduct3(rj,rk, rjk); |
273 |
+ |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
274 |
+ |
|
275 |
+ |
crossProduct3(rk,ri, rki); |
276 |
+ |
distZX = dotProduct3(rj,rki) / norm3(rki); |
277 |
+ |
|
278 |
+ |
minDist = min(min(distXY, distYZ), distZX); |
279 |
+ |
return minDist/2; |
280 |
+ |
|
281 |
+ |
} |
282 |
+ |
|
283 |
|
void SimInfo::wrapVector( double thePos[3] ){ |
284 |
|
|
285 |
< |
int i, j, k; |
285 |
> |
int i; |
286 |
|
double scaled[3]; |
287 |
|
|
288 |
|
if( !orthoRhombic ){ |
320 |
|
|
321 |
|
|
322 |
|
int SimInfo::getNDF(){ |
323 |
< |
int ndf_local, ndf; |
324 |
< |
|
325 |
< |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
323 |
> |
int ndf_local; |
324 |
> |
|
325 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
326 |
> |
ndf_local += 3; |
327 |
> |
if (integrableObjects[i]->isDirectional()) |
328 |
> |
ndf_local += 3; |
329 |
> |
} |
330 |
|
|
331 |
+ |
// n_constraints is local, so subtract them on each processor: |
332 |
+ |
|
333 |
+ |
ndf_local -= n_constraints; |
334 |
+ |
|
335 |
|
#ifdef IS_MPI |
336 |
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
337 |
|
#else |
338 |
|
ndf = ndf_local; |
339 |
|
#endif |
340 |
|
|
341 |
+ |
// nZconstraints is global, as are the 3 COM translations for the |
342 |
+ |
// entire system: |
343 |
+ |
|
344 |
|
ndf = ndf - 3 - nZconstraints; |
345 |
|
|
346 |
|
return ndf; |
347 |
|
} |
348 |
|
|
349 |
|
int SimInfo::getNDFraw() { |
350 |
< |
int ndfRaw_local, ndfRaw; |
350 |
> |
int ndfRaw_local; |
351 |
|
|
352 |
|
// Raw degrees of freedom that we have to set |
353 |
< |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
354 |
< |
|
353 |
> |
|
354 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
355 |
> |
ndfRaw_local += 3; |
356 |
> |
if (integrableObjects[i]->isDirectional()) |
357 |
> |
ndfRaw_local += 3; |
358 |
> |
} |
359 |
> |
|
360 |
|
#ifdef IS_MPI |
361 |
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
362 |
|
#else |
365 |
|
|
366 |
|
return ndfRaw; |
367 |
|
} |
368 |
< |
|
368 |
> |
|
369 |
> |
int SimInfo::getNDFtranslational() { |
370 |
> |
int ndfTrans_local; |
371 |
> |
|
372 |
> |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
373 |
> |
|
374 |
> |
|
375 |
> |
#ifdef IS_MPI |
376 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
377 |
> |
#else |
378 |
> |
ndfTrans = ndfTrans_local; |
379 |
> |
#endif |
380 |
> |
|
381 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
382 |
> |
|
383 |
> |
return ndfTrans; |
384 |
> |
} |
385 |
> |
|
386 |
> |
int SimInfo::getTotIntegrableObjects() { |
387 |
> |
int nObjs_local; |
388 |
> |
int nObjs; |
389 |
> |
|
390 |
> |
nObjs_local = integrableObjects.size(); |
391 |
> |
|
392 |
> |
|
393 |
> |
#ifdef IS_MPI |
394 |
> |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
395 |
> |
#else |
396 |
> |
nObjs = nObjs_local; |
397 |
> |
#endif |
398 |
> |
|
399 |
> |
|
400 |
> |
return nObjs; |
401 |
> |
} |
402 |
> |
|
403 |
|
void SimInfo::refreshSim(){ |
404 |
|
|
405 |
|
simtype fInfo; |
409 |
|
|
410 |
|
fInfo.dielect = 0.0; |
411 |
|
|
412 |
< |
if( useDipole ){ |
412 |
> |
if( useDipoles ){ |
413 |
|
if( useReactionField )fInfo.dielect = dielectric; |
414 |
|
} |
415 |
|
|
418 |
|
fInfo.SIM_uses_LJ = useLJ; |
419 |
|
fInfo.SIM_uses_sticky = useSticky; |
420 |
|
//fInfo.SIM_uses_sticky = 0; |
421 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
421 |
> |
fInfo.SIM_uses_charges = useCharges; |
422 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
423 |
|
//fInfo.SIM_uses_dipoles = 0; |
424 |
< |
//fInfo.SIM_uses_RF = useReactionField; |
425 |
< |
fInfo.SIM_uses_RF = 0; |
424 |
> |
fInfo.SIM_uses_RF = useReactionField; |
425 |
> |
//fInfo.SIM_uses_RF = 0; |
426 |
|
fInfo.SIM_uses_GB = useGB; |
427 |
|
fInfo.SIM_uses_EAM = useEAM; |
428 |
|
|
429 |
< |
excl = Exclude::getArray(); |
429 |
> |
n_exclude = excludes->getSize(); |
430 |
> |
excl = excludes->getFortranArray(); |
431 |
|
|
432 |
|
#ifdef IS_MPI |
433 |
|
n_global = mpiSim->getTotAtoms(); |
457 |
|
|
458 |
|
this->ndf = this->getNDF(); |
459 |
|
this->ndfRaw = this->getNDFraw(); |
460 |
< |
|
460 |
> |
this->ndfTrans = this->getNDFtranslational(); |
461 |
|
} |
462 |
|
|
463 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
464 |
|
|
465 |
< |
void SimInfo::setRcut( double theRcut ){ |
465 |
> |
haveRcut = 1; |
466 |
> |
rCut = theRcut; |
467 |
|
|
468 |
< |
if( !haveOrigRcut ){ |
451 |
< |
haveOrigRcut = 1; |
452 |
< |
origRcut = theRcut; |
453 |
< |
} |
468 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
469 |
|
|
470 |
< |
rCut = theRcut; |
456 |
< |
checkCutOffs(); |
470 |
> |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
471 |
|
} |
472 |
|
|
473 |
< |
void SimInfo::setEcr( double theEcr ){ |
473 |
> |
void SimInfo::setDefaultEcr( double theEcr ){ |
474 |
|
|
475 |
< |
if( !haveOrigEcr ){ |
462 |
< |
haveOrigEcr = 1; |
463 |
< |
origEcr = theEcr; |
464 |
< |
} |
465 |
< |
|
475 |
> |
haveEcr = 1; |
476 |
|
ecr = theEcr; |
477 |
< |
checkCutOffs(); |
477 |
> |
|
478 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
479 |
> |
|
480 |
> |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
481 |
|
} |
482 |
|
|
483 |
< |
void SimInfo::setEcr( double theEcr, double theEst ){ |
483 |
> |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
484 |
|
|
485 |
|
est = theEst; |
486 |
< |
setEcr( theEcr ); |
486 |
> |
setDefaultEcr( theEcr ); |
487 |
|
} |
488 |
|
|
489 |
|
|
490 |
|
void SimInfo::checkCutOffs( void ){ |
491 |
< |
|
479 |
< |
int cutChanged = 0; |
480 |
< |
|
481 |
< |
|
482 |
< |
|
491 |
> |
|
492 |
|
if( boxIsInit ){ |
493 |
|
|
494 |
|
//we need to check cutOffs against the box |
495 |
< |
|
496 |
< |
if(( maxCutoff > rCut )&&(usePBC)){ |
497 |
< |
if( rCut < origRcut ){ |
498 |
< |
rCut = origRcut; |
499 |
< |
if (rCut > maxCutoff) rCut = maxCutoff; |
500 |
< |
|
501 |
< |
sprintf( painCave.errMsg, |
502 |
< |
"New Box size is setting the long range cutoff radius " |
503 |
< |
"to %lf\n", |
504 |
< |
rCut ); |
505 |
< |
painCave.isFatal = 0; |
506 |
< |
simError(); |
507 |
< |
} |
495 |
> |
|
496 |
> |
if( rCut > maxCutoff ){ |
497 |
> |
sprintf( painCave.errMsg, |
498 |
> |
"LJrcut is too large for the current periodic box.\n" |
499 |
> |
"\tCurrent Value of LJrcut = %G at time %G\n " |
500 |
> |
"\tThis is larger than half of at least one of the\n" |
501 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
502 |
> |
"\n, %G" |
503 |
> |
"\t[ %G %G %G ]\n" |
504 |
> |
"\t[ %G %G %G ]\n" |
505 |
> |
"\t[ %G %G %G ]\n", |
506 |
> |
rCut, currentTime, maxCutoff, |
507 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
508 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
509 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
510 |
> |
painCave.isFatal = 1; |
511 |
> |
simError(); |
512 |
|
} |
513 |
< |
|
514 |
< |
if( maxCutoff > ecr ){ |
515 |
< |
if( ecr < origEcr ){ |
503 |
< |
rCut = origEcr; |
504 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
505 |
< |
|
513 |
> |
|
514 |
> |
if( haveEcr ){ |
515 |
> |
if( ecr > maxCutoff ){ |
516 |
|
sprintf( painCave.errMsg, |
517 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
518 |
< |
"to %lf\n", |
519 |
< |
ecr ); |
520 |
< |
painCave.isFatal = 0; |
517 |
> |
"electrostaticCutoffRadius is too large for the current\n" |
518 |
> |
"\tperiodic box.\n\n" |
519 |
> |
"\tCurrent Value of ECR = %G at time %G\n " |
520 |
> |
"\tThis is larger than half of at least one of the\n" |
521 |
> |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
522 |
> |
"\n" |
523 |
> |
"\t[ %G %G %G ]\n" |
524 |
> |
"\t[ %G %G %G ]\n" |
525 |
> |
"\t[ %G %G %G ]\n", |
526 |
> |
ecr, currentTime, |
527 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
528 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
529 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
530 |
> |
painCave.isFatal = 1; |
531 |
|
simError(); |
532 |
|
} |
533 |
|
} |
534 |
< |
|
535 |
< |
|
536 |
< |
if ((rCut > maxCutoff)&&(usePBC)) { |
537 |
< |
sprintf( painCave.errMsg, |
538 |
< |
"New Box size is setting the long range cutoff radius " |
539 |
< |
"to %lf\n", |
540 |
< |
maxCutoff ); |
521 |
< |
painCave.isFatal = 0; |
522 |
< |
simError(); |
523 |
< |
rCut = maxCutoff; |
524 |
< |
} |
525 |
< |
|
526 |
< |
if( ecr > maxCutoff){ |
527 |
< |
sprintf( painCave.errMsg, |
528 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
529 |
< |
"to %lf\n", |
530 |
< |
maxCutoff ); |
531 |
< |
painCave.isFatal = 0; |
532 |
< |
simError(); |
533 |
< |
ecr = maxCutoff; |
534 |
< |
} |
535 |
< |
|
536 |
< |
|
534 |
> |
} else { |
535 |
> |
// initialize this stuff before using it, OK? |
536 |
> |
sprintf( painCave.errMsg, |
537 |
> |
"Trying to check cutoffs without a box.\n" |
538 |
> |
"\tOOPSE should have better programmers than that.\n" ); |
539 |
> |
painCave.isFatal = 1; |
540 |
> |
simError(); |
541 |
|
} |
538 |
– |
|
539 |
– |
|
540 |
– |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
541 |
– |
|
542 |
– |
// rlist is the 1.0 plus max( rcut, ecr ) |
542 |
|
|
544 |
– |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
545 |
– |
|
546 |
– |
if( cutChanged ){ |
547 |
– |
|
548 |
– |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
549 |
– |
} |
550 |
– |
|
551 |
– |
oldEcr = ecr; |
552 |
– |
oldRcut = rCut; |
543 |
|
} |
544 |
|
|
545 |
|
void SimInfo::addProperty(GenericData* prop){ |
588 |
|
|
589 |
|
return result; |
590 |
|
} |
601 |
– |
|
602 |
– |
|