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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> |
3 |
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#include <math.h> |
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|
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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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} |
24 |
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|
25 |
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inline double min( double a, double b ){ |
26 |
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return (a < b ) ? a : b; |
27 |
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} |
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|
29 |
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SimInfo* currentInfo; |
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|
31 |
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SimInfo::SimInfo(){ |
32 |
< |
excludes = NULL; |
32 |
> |
|
33 |
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n_constraints = 0; |
34 |
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nZconstraints = 0; |
35 |
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n_oriented = 0; |
36 |
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n_dipoles = 0; |
37 |
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ndf = 0; |
38 |
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ndfRaw = 0; |
39 |
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nZconstraints = 0; |
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the_integrator = NULL; |
41 |
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setTemp = 0; |
42 |
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thermalTime = 0.0; |
43 |
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currentTime = 0.0; |
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rCut = 0.0; |
45 |
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ecr = 0.0; |
46 |
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est = 0.0; |
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|
48 |
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haveRcut = 0; |
49 |
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haveEcr = 0; |
50 |
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boxIsInit = 0; |
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|
52 |
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resetTime = 1e99; |
53 |
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|
54 |
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orthoRhombic = 0; |
55 |
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orthoTolerance = 1E-6; |
56 |
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useInitXSstate = true; |
57 |
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|
58 |
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usePBC = 0; |
59 |
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useLJ = 0; |
60 |
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useSticky = 0; |
61 |
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useDipole = 0; |
61 |
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useCharges = 0; |
62 |
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useDipoles = 0; |
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useReactionField = 0; |
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useGB = 0; |
65 |
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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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|
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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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|
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|
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SimInfo::~SimInfo(){ |
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|
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delete myConfiguration; |
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|
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map<string, GenericData*>::iterator i; |
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|
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for(i = properties.begin(); i != properties.end(); i++) |
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delete (*i).second; |
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|
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} |
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|
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void SimInfo::setBox(double newBox[3]) { |
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int i, j; |
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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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if( !boxIsInit ) boxIsInit = 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++) Hmat[i][j] = theBox[i][j]; |
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|
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// cerr |
81 |
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// << "setting Hmat ->\n" |
82 |
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// << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
83 |
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// << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
84 |
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// << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
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|
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calcBoxL(); |
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calcHmatInv(); |
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|
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|
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setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
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|
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
100 |
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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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|
102 |
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maxCutoff = smallestBoxL / 2.0; |
103 |
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|
104 |
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if (rList > maxCutoff) { |
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sprintf( painCave.errMsg, |
106 |
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"New Box size is forcing neighborlist radius down to %lf\n", |
107 |
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maxCutoff ); |
108 |
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painCave.isFatal = 0; |
109 |
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simError(); |
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|
111 |
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rList = maxCutoff; |
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|
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sprintf( painCave.errMsg, |
114 |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff - 1.0 ); |
116 |
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painCave.isFatal = 0; |
117 |
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simError(); |
118 |
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|
119 |
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rCut = rList - 1.0; |
120 |
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|
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// list radius changed so we have to refresh the simulation structure. |
122 |
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refreshSim(); |
123 |
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} |
124 |
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|
125 |
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if (rCut > maxCutoff) { |
126 |
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sprintf( painCave.errMsg, |
127 |
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"New Box size is forcing cutoff radius down to %lf\n", |
128 |
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maxCutoff ); |
129 |
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painCave.isFatal = 0; |
130 |
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simError(); |
131 |
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|
132 |
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status = 0; |
133 |
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LJ_new_rcut(&rCut, &status); |
134 |
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if (status != 0) { |
135 |
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sprintf( painCave.errMsg, |
136 |
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"Error in recomputing LJ shifts based on new rcut\n"); |
137 |
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painCave.isFatal = 1; |
138 |
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simError(); |
139 |
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} |
140 |
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} |
132 |
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} |
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|
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|
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|
156 |
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void SimInfo::calcHmatInv( void ) { |
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|
158 |
+ |
int oldOrtho; |
159 |
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int i,j; |
160 |
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double smallDiag; |
161 |
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double tol; |
163 |
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|
164 |
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invertMat3( Hmat, HmatInv ); |
165 |
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|
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// Check the inverse to make sure it is sane: |
175 |
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|
176 |
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matMul3( Hmat, HmatInv, sanity ); |
177 |
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|
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// check to see if Hmat is orthorhombic |
167 |
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|
168 |
< |
smallDiag = Hmat[0][0]; |
181 |
< |
if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1]; |
182 |
< |
if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2]; |
183 |
< |
tol = smallDiag * 1E-6; |
168 |
> |
oldOrtho = orthoRhombic; |
169 |
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|
170 |
+ |
smallDiag = fabs(Hmat[0][0]); |
171 |
+ |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
172 |
+ |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
173 |
+ |
tol = smallDiag * orthoTolerance; |
174 |
+ |
|
175 |
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orthoRhombic = 1; |
176 |
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|
177 |
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for (i = 0; i < 3; i++ ) { |
178 |
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for (j = 0 ; j < 3; j++) { |
179 |
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if (i != j) { |
180 |
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if (orthoRhombic) { |
181 |
< |
if (Hmat[i][j] >= tol) orthoRhombic = 0; |
181 |
> |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
182 |
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} |
183 |
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} |
184 |
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} |
185 |
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} |
196 |
– |
} |
186 |
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|
187 |
< |
double SimInfo::matDet3(double a[3][3]) { |
188 |
< |
int i, j, k; |
189 |
< |
double determinant; |
190 |
< |
|
191 |
< |
determinant = 0.0; |
192 |
< |
|
193 |
< |
for(i = 0; i < 3; i++) { |
194 |
< |
j = (i+1)%3; |
195 |
< |
k = (i+2)%3; |
196 |
< |
|
197 |
< |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
209 |
< |
} |
210 |
< |
|
211 |
< |
return determinant; |
212 |
< |
} |
213 |
< |
|
214 |
< |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
215 |
< |
|
216 |
< |
int i, j, k, l, m, n; |
217 |
< |
double determinant; |
218 |
< |
|
219 |
< |
determinant = matDet3( a ); |
220 |
< |
|
221 |
< |
if (determinant == 0.0) { |
222 |
< |
sprintf( painCave.errMsg, |
223 |
< |
"Can't invert a matrix with a zero determinant!\n"); |
224 |
< |
painCave.isFatal = 1; |
225 |
< |
simError(); |
226 |
< |
} |
227 |
< |
|
228 |
< |
for (i=0; i < 3; i++) { |
229 |
< |
j = (i+1)%3; |
230 |
< |
k = (i+2)%3; |
231 |
< |
for(l = 0; l < 3; l++) { |
232 |
< |
m = (l+1)%3; |
233 |
< |
n = (l+2)%3; |
234 |
< |
|
235 |
< |
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 |
|
} |
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 |
< |
|
247 |
< |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
248 |
< |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
249 |
< |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
250 |
< |
|
251 |
< |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
252 |
< |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
253 |
< |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
254 |
< |
|
255 |
< |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
256 |
< |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
257 |
< |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
258 |
< |
} |
259 |
< |
|
260 |
< |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
261 |
< |
double a0, a1, a2; |
262 |
< |
|
263 |
< |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
264 |
< |
|
265 |
< |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
266 |
< |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
267 |
< |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
268 |
< |
} |
269 |
< |
|
270 |
< |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
271 |
< |
double temp[3][3]; |
272 |
< |
int i, j; |
273 |
< |
|
274 |
< |
for (i = 0; i < 3; i++) { |
275 |
< |
for (j = 0; j < 3; j++) { |
276 |
< |
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 |
|
} |
279 |
– |
for (i = 0; i < 3; i++) { |
280 |
– |
for (j = 0; j < 3; j++) { |
281 |
– |
out[i][j] = temp[i][j]; |
282 |
– |
} |
283 |
– |
} |
211 |
|
} |
285 |
– |
|
286 |
– |
void SimInfo::printMat3(double A[3][3] ){ |
212 |
|
|
288 |
– |
std::cerr |
289 |
– |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
290 |
– |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
291 |
– |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
292 |
– |
} |
293 |
– |
|
294 |
– |
void SimInfo::printMat9(double A[9] ){ |
295 |
– |
|
296 |
– |
std::cerr |
297 |
– |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
298 |
– |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
299 |
– |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
300 |
– |
} |
301 |
– |
|
213 |
|
void SimInfo::calcBoxL( void ){ |
214 |
|
|
215 |
|
double dx, dy, dz, dsq; |
305 |
– |
int i; |
216 |
|
|
217 |
|
// boxVol = Determinant of Hmat |
218 |
|
|
222 |
|
|
223 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
224 |
|
dsq = dx*dx + dy*dy + dz*dz; |
225 |
< |
boxLx = sqrt( dsq ); |
225 |
> |
boxL[0] = sqrt( dsq ); |
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 |
< |
boxLy = sqrt( dsq ); |
232 |
> |
boxL[1] = sqrt( dsq ); |
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 |
< |
boxLz = sqrt( dsq ); |
240 |
> |
boxL[2] = sqrt( dsq ); |
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; |
323 |
> |
int ndf_local; |
324 |
> |
|
325 |
> |
ndf_local = 0; |
326 |
|
|
327 |
< |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
327 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
328 |
> |
ndf_local += 3; |
329 |
> |
if (integrableObjects[i]->isDirectional()) { |
330 |
> |
if (integrableObjects[i]->isLinear()) |
331 |
> |
ndf_local += 2; |
332 |
> |
else |
333 |
> |
ndf_local += 3; |
334 |
> |
} |
335 |
> |
} |
336 |
|
|
337 |
+ |
// n_constraints is local, so subtract them on each processor: |
338 |
+ |
|
339 |
+ |
ndf_local -= n_constraints; |
340 |
+ |
|
341 |
|
#ifdef IS_MPI |
342 |
|
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
343 |
|
#else |
344 |
|
ndf = ndf_local; |
345 |
|
#endif |
346 |
|
|
347 |
< |
ndf = ndf - 3; |
347 |
> |
// nZconstraints is global, as are the 3 COM translations for the |
348 |
> |
// entire system: |
349 |
|
|
350 |
+ |
ndf = ndf - 3 - nZconstraints; |
351 |
+ |
|
352 |
|
return ndf; |
353 |
|
} |
354 |
|
|
355 |
|
int SimInfo::getNDFraw() { |
356 |
< |
int ndfRaw_local, ndfRaw; |
356 |
> |
int ndfRaw_local; |
357 |
|
|
358 |
|
// Raw degrees of freedom that we have to set |
359 |
< |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
360 |
< |
|
359 |
> |
ndfRaw_local = 0; |
360 |
> |
|
361 |
> |
for(int i = 0; i < integrableObjects.size(); i++){ |
362 |
> |
ndfRaw_local += 3; |
363 |
> |
if (integrableObjects[i]->isDirectional()) { |
364 |
> |
if (integrableObjects[i]->isLinear()) |
365 |
> |
ndfRaw_local += 2; |
366 |
> |
else |
367 |
> |
ndfRaw_local += 3; |
368 |
> |
} |
369 |
> |
} |
370 |
> |
|
371 |
|
#ifdef IS_MPI |
372 |
|
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
373 |
|
#else |
376 |
|
|
377 |
|
return ndfRaw; |
378 |
|
} |
379 |
< |
|
379 |
> |
|
380 |
> |
int SimInfo::getNDFtranslational() { |
381 |
> |
int ndfTrans_local; |
382 |
> |
|
383 |
> |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
384 |
> |
|
385 |
> |
|
386 |
> |
#ifdef IS_MPI |
387 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
388 |
> |
#else |
389 |
> |
ndfTrans = ndfTrans_local; |
390 |
> |
#endif |
391 |
> |
|
392 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
393 |
> |
|
394 |
> |
return ndfTrans; |
395 |
> |
} |
396 |
> |
|
397 |
> |
int SimInfo::getTotIntegrableObjects() { |
398 |
> |
int nObjs_local; |
399 |
> |
int nObjs; |
400 |
> |
|
401 |
> |
nObjs_local = integrableObjects.size(); |
402 |
> |
|
403 |
> |
|
404 |
> |
#ifdef IS_MPI |
405 |
> |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
406 |
> |
#else |
407 |
> |
nObjs = nObjs_local; |
408 |
> |
#endif |
409 |
> |
|
410 |
> |
|
411 |
> |
return nObjs; |
412 |
> |
} |
413 |
> |
|
414 |
|
void SimInfo::refreshSim(){ |
415 |
|
|
416 |
|
simtype fInfo; |
417 |
|
int isError; |
418 |
|
int n_global; |
419 |
|
int* excl; |
420 |
< |
|
409 |
< |
fInfo.rrf = 0.0; |
410 |
< |
fInfo.rt = 0.0; |
420 |
> |
|
421 |
|
fInfo.dielect = 0.0; |
422 |
|
|
423 |
< |
fInfo.rlist = rList; |
414 |
< |
fInfo.rcut = rCut; |
415 |
< |
|
416 |
< |
if( useDipole ){ |
417 |
< |
fInfo.rrf = ecr; |
418 |
< |
fInfo.rt = ecr - est; |
423 |
> |
if( useDipoles ){ |
424 |
|
if( useReactionField )fInfo.dielect = dielectric; |
425 |
|
} |
426 |
|
|
429 |
|
fInfo.SIM_uses_LJ = useLJ; |
430 |
|
fInfo.SIM_uses_sticky = useSticky; |
431 |
|
//fInfo.SIM_uses_sticky = 0; |
432 |
< |
fInfo.SIM_uses_dipoles = useDipole; |
432 |
> |
fInfo.SIM_uses_charges = useCharges; |
433 |
> |
fInfo.SIM_uses_dipoles = useDipoles; |
434 |
|
//fInfo.SIM_uses_dipoles = 0; |
435 |
< |
//fInfo.SIM_uses_RF = useReactionField; |
436 |
< |
fInfo.SIM_uses_RF = 0; |
435 |
> |
fInfo.SIM_uses_RF = useReactionField; |
436 |
> |
//fInfo.SIM_uses_RF = 0; |
437 |
|
fInfo.SIM_uses_GB = useGB; |
438 |
|
fInfo.SIM_uses_EAM = useEAM; |
439 |
|
|
440 |
< |
excl = Exclude::getArray(); |
440 |
> |
n_exclude = excludes->getSize(); |
441 |
> |
excl = excludes->getFortranArray(); |
442 |
|
|
443 |
|
#ifdef IS_MPI |
444 |
|
n_global = mpiSim->getTotAtoms(); |
468 |
|
|
469 |
|
this->ndf = this->getNDF(); |
470 |
|
this->ndfRaw = this->getNDFraw(); |
471 |
+ |
this->ndfTrans = this->getNDFtranslational(); |
472 |
+ |
} |
473 |
|
|
474 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
475 |
+ |
|
476 |
+ |
haveRcut = 1; |
477 |
+ |
rCut = theRcut; |
478 |
+ |
|
479 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
480 |
+ |
|
481 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
482 |
|
} |
483 |
|
|
484 |
+ |
void SimInfo::setDefaultEcr( double theEcr ){ |
485 |
+ |
|
486 |
+ |
haveEcr = 1; |
487 |
+ |
ecr = theEcr; |
488 |
+ |
|
489 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
490 |
+ |
|
491 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
492 |
+ |
} |
493 |
+ |
|
494 |
+ |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
495 |
+ |
|
496 |
+ |
est = theEst; |
497 |
+ |
setDefaultEcr( theEcr ); |
498 |
+ |
} |
499 |
+ |
|
500 |
+ |
|
501 |
+ |
void SimInfo::checkCutOffs( void ){ |
502 |
+ |
|
503 |
+ |
if( boxIsInit ){ |
504 |
+ |
|
505 |
+ |
//we need to check cutOffs against the box |
506 |
+ |
|
507 |
+ |
if( rCut > maxCutoff ){ |
508 |
+ |
sprintf( painCave.errMsg, |
509 |
+ |
"LJrcut is too large for the current periodic box.\n" |
510 |
+ |
"\tCurrent Value of LJrcut = %G at time %G\n " |
511 |
+ |
"\tThis is larger than half of at least one of the\n" |
512 |
+ |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
513 |
+ |
"\n" |
514 |
+ |
"\t[ %G %G %G ]\n" |
515 |
+ |
"\t[ %G %G %G ]\n" |
516 |
+ |
"\t[ %G %G %G ]\n", |
517 |
+ |
rCut, currentTime, |
518 |
+ |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
519 |
+ |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
520 |
+ |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
521 |
+ |
painCave.isFatal = 1; |
522 |
+ |
simError(); |
523 |
+ |
} |
524 |
+ |
|
525 |
+ |
if( haveEcr ){ |
526 |
+ |
if( ecr > maxCutoff ){ |
527 |
+ |
sprintf( painCave.errMsg, |
528 |
+ |
"electrostaticCutoffRadius is too large for the current\n" |
529 |
+ |
"\tperiodic box.\n\n" |
530 |
+ |
"\tCurrent Value of ECR = %G at time %G\n " |
531 |
+ |
"\tThis is larger than half of at least one of the\n" |
532 |
+ |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
533 |
+ |
"\n" |
534 |
+ |
"\t[ %G %G %G ]\n" |
535 |
+ |
"\t[ %G %G %G ]\n" |
536 |
+ |
"\t[ %G %G %G ]\n", |
537 |
+ |
ecr, currentTime, |
538 |
+ |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
539 |
+ |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
540 |
+ |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
541 |
+ |
painCave.isFatal = 1; |
542 |
+ |
simError(); |
543 |
+ |
} |
544 |
+ |
} |
545 |
+ |
} else { |
546 |
+ |
// initialize this stuff before using it, OK? |
547 |
+ |
sprintf( painCave.errMsg, |
548 |
+ |
"Trying to check cutoffs without a box.\n" |
549 |
+ |
"\tOOPSE should have better programmers than that.\n" ); |
550 |
+ |
painCave.isFatal = 1; |
551 |
+ |
simError(); |
552 |
+ |
} |
553 |
+ |
|
554 |
+ |
} |
555 |
+ |
|
556 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
557 |
+ |
|
558 |
+ |
map<string, GenericData*>::iterator result; |
559 |
+ |
result = properties.find(prop->getID()); |
560 |
+ |
|
561 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
562 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
563 |
+ |
|
564 |
+ |
if(result != properties.end()){ |
565 |
+ |
|
566 |
+ |
delete (*result).second; |
567 |
+ |
(*result).second = prop; |
568 |
+ |
|
569 |
+ |
} |
570 |
+ |
else{ |
571 |
+ |
|
572 |
+ |
properties[prop->getID()] = prop; |
573 |
+ |
|
574 |
+ |
} |
575 |
+ |
|
576 |
+ |
} |
577 |
+ |
|
578 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
579 |
+ |
|
580 |
+ |
map<string, GenericData*>::iterator result; |
581 |
+ |
|
582 |
+ |
//string lowerCaseName = (); |
583 |
+ |
|
584 |
+ |
result = properties.find(propName); |
585 |
+ |
|
586 |
+ |
if(result != properties.end()) |
587 |
+ |
return (*result).second; |
588 |
+ |
else |
589 |
+ |
return NULL; |
590 |
+ |
} |
591 |
+ |
|