1 |
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#include <cstdlib> |
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#include <cstring> |
3 |
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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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SimInfo::SimInfo(){ |
27 |
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excludes = NULL; |
28 |
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n_constraints = 0; |
29 |
+ |
nZconstraints = 0; |
30 |
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n_oriented = 0; |
31 |
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n_dipoles = 0; |
32 |
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ndf = 0; |
33 |
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ndfRaw = 0; |
34 |
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nZconstraints = 0; |
35 |
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the_integrator = NULL; |
36 |
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setTemp = 0; |
37 |
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thermalTime = 0.0; |
38 |
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currentTime = 0.0; |
39 |
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rCut = 0.0; |
40 |
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origRcut = -1.0; |
41 |
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ecr = 0.0; |
42 |
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origEcr = -1.0; |
43 |
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est = 0.0; |
44 |
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oldEcr = 0.0; |
45 |
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oldRcut = 0.0; |
46 |
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|
47 |
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haveOrigRcut = 0; |
48 |
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haveOrigEcr = 0; |
49 |
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boxIsInit = 0; |
50 |
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|
51 |
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resetTime = 1e99; |
52 |
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|
53 |
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|
54 |
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usePBC = 0; |
55 |
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useLJ = 0; |
56 |
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useSticky = 0; |
59 |
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useGB = 0; |
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useEAM = 0; |
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|
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myConfiguration = new SimState(); |
63 |
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|
64 |
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wrapMeSimInfo( this ); |
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} |
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|
49 |
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void SimInfo::setBox(double newBox[3]) { |
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|
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double smallestBoxL, maxCutoff; |
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int status; |
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int i; |
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SimInfo::~SimInfo(){ |
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|
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for(i=0; i<9; i++) Hmat[i] = 0.0;; |
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delete myConfiguration; |
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|
72 |
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Hmat[0] = newBox[0]; |
73 |
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Hmat[4] = newBox[1]; |
74 |
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Hmat[8] = newBox[2]; |
72 |
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map<string, GenericData*>::iterator i; |
73 |
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|
74 |
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for(i = properties.begin(); i != properties.end(); i++) |
75 |
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delete (*i).second; |
76 |
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|
77 |
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} |
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|
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calcHmatI(); |
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calcBoxL(); |
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void SimInfo::setBox(double newBox[3]) { |
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|
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int i, j; |
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double tempMat[3][3]; |
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|
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setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
84 |
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for(i=0; i<3; i++) |
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for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
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|
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smallestBoxL = boxLx; |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
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tempMat[0][0] = newBox[0]; |
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tempMat[1][1] = newBox[1]; |
89 |
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tempMat[2][2] = newBox[2]; |
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|
91 |
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maxCutoff = smallestBoxL / 2.0; |
91 |
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setBoxM( tempMat ); |
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|
93 |
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if (rList > maxCutoff) { |
73 |
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sprintf( painCave.errMsg, |
74 |
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"New Box size is forcing neighborlist radius down to %lf\n", |
75 |
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maxCutoff ); |
76 |
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painCave.isFatal = 0; |
77 |
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simError(); |
93 |
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} |
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|
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rList = maxCutoff; |
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void SimInfo::setBoxM( double theBox[3][3] ){ |
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|
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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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// [ 1 4 7 ] |
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// [ 2 5 8 ] |
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double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
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|
105 |
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sprintf( painCave.errMsg, |
106 |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff - 1.0 ); |
84 |
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painCave.isFatal = 0; |
85 |
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simError(); |
105 |
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|
106 |
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if( !boxIsInit ) boxIsInit = 1; |
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|
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rCut = rList - 1.0; |
108 |
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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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calcBoxL(); |
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calcHmatInv(); |
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|
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// list radius changed so we have to refresh the simulation structure. |
115 |
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refreshSim(); |
114 |
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for(i=0; i < 3; i++) { |
115 |
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for (j=0; j < 3; j++) { |
116 |
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FortranHmat[3*j + i] = Hmat[i][j]; |
117 |
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FortranHmatInv[3*j + i] = HmatInv[i][j]; |
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} |
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} |
120 |
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|
121 |
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if (rCut > maxCutoff) { |
122 |
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sprintf( painCave.errMsg, |
123 |
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"New Box size is forcing cutoff radius down to %lf\n", |
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maxCutoff ); |
97 |
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painCave.isFatal = 0; |
98 |
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simError(); |
121 |
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setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
122 |
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|
123 |
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} |
124 |
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|
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|
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status = 0; |
127 |
< |
LJ_new_rcut(&rCut, &status); |
128 |
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if (status != 0) { |
129 |
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sprintf( painCave.errMsg, |
130 |
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"Error in recomputing LJ shifts based on new rcut\n"); |
105 |
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painCave.isFatal = 1; |
106 |
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simError(); |
107 |
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} |
108 |
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} |
126 |
> |
void SimInfo::getBoxM (double theBox[3][3]) { |
127 |
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|
128 |
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int i, j; |
129 |
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for(i=0; i<3; i++) |
130 |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
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} |
132 |
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|
111 |
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void SimInfo::setBoxM( double theBox[9] ){ |
112 |
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|
113 |
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int i, status; |
114 |
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double smallestBoxL, maxCutoff; |
133 |
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|
134 |
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for(i=0; i<9; i++) Hmat[i] = theBox[i]; |
135 |
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calcHmatI(); |
136 |
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calcBoxL(); |
134 |
> |
void SimInfo::scaleBox(double scale) { |
135 |
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double theBox[3][3]; |
136 |
> |
int i, j; |
137 |
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|
138 |
< |
setFortranBoxSize(Hmat, HmatI, &orthoRhombic); |
121 |
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|
122 |
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smallestBoxL = boxLx; |
123 |
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if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
124 |
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if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
138 |
> |
// cerr << "Scaling box by " << scale << "\n"; |
139 |
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|
140 |
< |
maxCutoff = smallestBoxL / 2.0; |
140 |
> |
for(i=0; i<3; i++) |
141 |
> |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
142 |
|
|
143 |
< |
if (rList > maxCutoff) { |
129 |
< |
sprintf( painCave.errMsg, |
130 |
< |
"New Box size is forcing neighborlist radius down to %lf\n", |
131 |
< |
maxCutoff ); |
132 |
< |
painCave.isFatal = 0; |
133 |
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simError(); |
143 |
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setBoxM(theBox); |
144 |
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|
145 |
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rList = maxCutoff; |
145 |
> |
} |
146 |
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|
147 |
< |
sprintf( painCave.errMsg, |
148 |
< |
"New Box size is forcing cutoff radius down to %lf\n", |
149 |
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maxCutoff - 1.0 ); |
150 |
< |
painCave.isFatal = 0; |
151 |
< |
simError(); |
147 |
> |
void SimInfo::calcHmatInv( void ) { |
148 |
> |
|
149 |
> |
int oldOrtho; |
150 |
> |
int i,j; |
151 |
> |
double smallDiag; |
152 |
> |
double tol; |
153 |
> |
double sanity[3][3]; |
154 |
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|
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rCut = rList - 1.0; |
155 |
> |
invertMat3( Hmat, HmatInv ); |
156 |
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|
157 |
< |
// list radius changed so we have to refresh the simulation structure. |
158 |
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refreshSim(); |
157 |
> |
// check to see if Hmat is orthorhombic |
158 |
> |
|
159 |
> |
oldOrtho = orthoRhombic; |
160 |
> |
|
161 |
> |
smallDiag = fabs(Hmat[0][0]); |
162 |
> |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
163 |
> |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
164 |
> |
tol = smallDiag * 1E-6; |
165 |
> |
|
166 |
> |
orthoRhombic = 1; |
167 |
> |
|
168 |
> |
for (i = 0; i < 3; i++ ) { |
169 |
> |
for (j = 0 ; j < 3; j++) { |
170 |
> |
if (i != j) { |
171 |
> |
if (orthoRhombic) { |
172 |
> |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
173 |
> |
} |
174 |
> |
} |
175 |
> |
} |
176 |
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} |
177 |
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|
178 |
< |
if (rCut > maxCutoff) { |
179 |
< |
sprintf( painCave.errMsg, |
180 |
< |
"New Box size is forcing cutoff radius down to %lf\n", |
181 |
< |
maxCutoff ); |
182 |
< |
painCave.isFatal = 0; |
183 |
< |
simError(); |
184 |
< |
|
185 |
< |
status = 0; |
186 |
< |
LJ_new_rcut(&rCut, &status); |
158 |
< |
if (status != 0) { |
178 |
> |
if( oldOrtho != orthoRhombic ){ |
179 |
> |
|
180 |
> |
if( orthoRhombic ){ |
181 |
> |
sprintf( painCave.errMsg, |
182 |
> |
"Hmat is switching from Non-Orthorhombic to OrthoRhombic\n" |
183 |
> |
" If this is a bad thing change the ortho tolerance in SimInfo.\n" ); |
184 |
> |
simError(); |
185 |
> |
} |
186 |
> |
else { |
187 |
|
sprintf( painCave.errMsg, |
188 |
< |
"Error in recomputing LJ shifts based on new rcut\n"); |
189 |
< |
painCave.isFatal = 1; |
188 |
> |
"Hmat is switching from Orthorhombic to Non-OrthoRhombic\n" |
189 |
> |
" If this is a bad thing change the ortho tolerance in SimInfo.\n" ); |
190 |
|
simError(); |
191 |
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} |
192 |
|
} |
193 |
|
} |
166 |
– |
|
194 |
|
|
195 |
< |
void SimInfo::getBoxM (double theBox[9]) { |
169 |
< |
|
170 |
< |
int i; |
171 |
< |
for(i=0; i<9; i++) theBox[i] = Hmat[i]; |
172 |
< |
} |
173 |
< |
|
174 |
< |
|
175 |
< |
void SimInfo::calcHmatI( void ) { |
176 |
< |
|
177 |
< |
double C[3][3]; |
178 |
< |
double detHmat; |
195 |
> |
double SimInfo::matDet3(double a[3][3]) { |
196 |
|
int i, j, k; |
197 |
< |
double smallDiag; |
181 |
< |
double tol; |
182 |
< |
double sanity[3][3]; |
197 |
> |
double determinant; |
198 |
|
|
199 |
< |
// calculate the adjunct of Hmat; |
199 |
> |
determinant = 0.0; |
200 |
|
|
201 |
< |
C[0][0] = ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]); |
202 |
< |
C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]); |
203 |
< |
C[2][0] = ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]); |
201 |
> |
for(i = 0; i < 3; i++) { |
202 |
> |
j = (i+1)%3; |
203 |
> |
k = (i+2)%3; |
204 |
|
|
205 |
< |
C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]); |
206 |
< |
C[1][1] = ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]); |
192 |
< |
C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]); |
205 |
> |
determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]); |
206 |
> |
} |
207 |
|
|
208 |
< |
C[0][2] = ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]); |
209 |
< |
C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]); |
196 |
< |
C[2][2] = ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]); |
208 |
> |
return determinant; |
209 |
> |
} |
210 |
|
|
211 |
< |
// calcutlate the determinant of Hmat |
211 |
> |
void SimInfo::invertMat3(double a[3][3], double b[3][3]) { |
212 |
|
|
213 |
< |
detHmat = 0.0; |
214 |
< |
for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0]; |
213 |
> |
int i, j, k, l, m, n; |
214 |
> |
double determinant; |
215 |
|
|
216 |
< |
|
204 |
< |
// H^-1 = C^T / det(H) |
205 |
< |
|
206 |
< |
i=0; |
207 |
< |
for(j=0; j<3; j++){ |
208 |
< |
for(k=0; k<3; k++){ |
216 |
> |
determinant = matDet3( a ); |
217 |
|
|
218 |
< |
HmatI[i] = C[j][k] / detHmat; |
219 |
< |
i++; |
220 |
< |
} |
218 |
> |
if (determinant == 0.0) { |
219 |
> |
sprintf( painCave.errMsg, |
220 |
> |
"Can't invert a matrix with a zero determinant!\n"); |
221 |
> |
painCave.isFatal = 1; |
222 |
> |
simError(); |
223 |
|
} |
224 |
|
|
225 |
< |
// sanity check |
226 |
< |
|
227 |
< |
for(i=0; i<3; i++){ |
228 |
< |
for(j=0; j<3; j++){ |
225 |
> |
for (i=0; i < 3; i++) { |
226 |
> |
j = (i+1)%3; |
227 |
> |
k = (i+2)%3; |
228 |
> |
for(l = 0; l < 3; l++) { |
229 |
> |
m = (l+1)%3; |
230 |
> |
n = (l+2)%3; |
231 |
|
|
232 |
< |
sanity[i][j] = 0.0; |
221 |
< |
for(k=0; k<3; k++){ |
222 |
< |
sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k]; |
223 |
< |
} |
232 |
> |
b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant; |
233 |
|
} |
234 |
|
} |
235 |
+ |
} |
236 |
|
|
237 |
< |
cerr << "sanity => \n" |
238 |
< |
<< sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n" |
229 |
< |
<< sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n" |
230 |
< |
<< sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2] |
231 |
< |
<< "\n"; |
232 |
< |
|
237 |
> |
void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) { |
238 |
> |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
239 |
|
|
240 |
< |
// check to see if Hmat is orthorhombic |
240 |
> |
r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0]; |
241 |
> |
r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1]; |
242 |
> |
r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2]; |
243 |
|
|
244 |
< |
smallDiag = Hmat[0]; |
245 |
< |
if(smallDiag > Hmat[4]) smallDiag = Hmat[4]; |
246 |
< |
if(smallDiag > Hmat[8]) smallDiag = Hmat[8]; |
247 |
< |
tol = smallDiag * 1E-6; |
244 |
> |
r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0]; |
245 |
> |
r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1]; |
246 |
> |
r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2]; |
247 |
> |
|
248 |
> |
r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0]; |
249 |
> |
r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1]; |
250 |
> |
r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2]; |
251 |
> |
|
252 |
> |
c[0][0] = r00; c[0][1] = r01; c[0][2] = r02; |
253 |
> |
c[1][0] = r10; c[1][1] = r11; c[1][2] = r12; |
254 |
> |
c[2][0] = r20; c[2][1] = r21; c[2][2] = r22; |
255 |
> |
} |
256 |
|
|
257 |
< |
orthoRhombic = 1; |
258 |
< |
for(i=0; (i<9) && orthoRhombic; i++){ |
259 |
< |
|
260 |
< |
if( (i%4) ){ // ignore the diagonals (0, 4, and 8) |
261 |
< |
orthoRhombic = (Hmat[i] <= tol); |
257 |
> |
void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) { |
258 |
> |
double a0, a1, a2; |
259 |
> |
|
260 |
> |
a0 = inVec[0]; a1 = inVec[1]; a2 = inVec[2]; |
261 |
> |
|
262 |
> |
outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2; |
263 |
> |
outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2; |
264 |
> |
outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2; |
265 |
> |
} |
266 |
> |
|
267 |
> |
void SimInfo::transposeMat3(double in[3][3], double out[3][3]) { |
268 |
> |
double temp[3][3]; |
269 |
> |
int i, j; |
270 |
> |
|
271 |
> |
for (i = 0; i < 3; i++) { |
272 |
> |
for (j = 0; j < 3; j++) { |
273 |
> |
temp[j][i] = in[i][j]; |
274 |
|
} |
275 |
|
} |
276 |
< |
|
276 |
> |
for (i = 0; i < 3; i++) { |
277 |
> |
for (j = 0; j < 3; j++) { |
278 |
> |
out[i][j] = temp[i][j]; |
279 |
> |
} |
280 |
> |
} |
281 |
> |
} |
282 |
> |
|
283 |
> |
void SimInfo::printMat3(double A[3][3] ){ |
284 |
> |
|
285 |
> |
std::cerr |
286 |
> |
<< "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n" |
287 |
> |
<< "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n" |
288 |
> |
<< "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n"; |
289 |
> |
} |
290 |
> |
|
291 |
> |
void SimInfo::printMat9(double A[9] ){ |
292 |
> |
|
293 |
> |
std::cerr |
294 |
> |
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
295 |
> |
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
296 |
> |
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
297 |
|
} |
298 |
|
|
299 |
+ |
|
300 |
+ |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
301 |
+ |
|
302 |
+ |
out[0] = a[1] * b[2] - a[2] * b[1]; |
303 |
+ |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
304 |
+ |
out[2] = a[0] * b[1] - a[1] * b[0]; |
305 |
+ |
|
306 |
+ |
} |
307 |
+ |
|
308 |
+ |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
309 |
+ |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
310 |
+ |
} |
311 |
+ |
|
312 |
+ |
double SimInfo::length3(double a[3]){ |
313 |
+ |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
314 |
+ |
} |
315 |
+ |
|
316 |
|
void SimInfo::calcBoxL( void ){ |
317 |
|
|
318 |
|
double dx, dy, dz, dsq; |
254 |
– |
int i; |
319 |
|
|
320 |
< |
// boxVol = h1 (dot) h2 (cross) h3 |
320 |
> |
// boxVol = Determinant of Hmat |
321 |
|
|
322 |
< |
boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
259 |
< |
+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
260 |
< |
+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
322 |
> |
boxVol = matDet3( Hmat ); |
323 |
|
|
262 |
– |
|
324 |
|
// boxLx |
325 |
|
|
326 |
< |
dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2]; |
326 |
> |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
327 |
|
dsq = dx*dx + dy*dy + dz*dz; |
328 |
< |
boxLx = sqrt( dsq ); |
328 |
> |
boxL[0] = sqrt( dsq ); |
329 |
> |
//maxCutoff = 0.5 * boxL[0]; |
330 |
|
|
331 |
|
// boxLy |
332 |
|
|
333 |
< |
dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5]; |
333 |
> |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
334 |
|
dsq = dx*dx + dy*dy + dz*dz; |
335 |
< |
boxLy = sqrt( dsq ); |
335 |
> |
boxL[1] = sqrt( dsq ); |
336 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
337 |
|
|
338 |
+ |
|
339 |
|
// boxLz |
340 |
|
|
341 |
< |
dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8]; |
341 |
> |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
342 |
|
dsq = dx*dx + dy*dy + dz*dz; |
343 |
< |
boxLz = sqrt( dsq ); |
343 |
> |
boxL[2] = sqrt( dsq ); |
344 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
345 |
> |
|
346 |
> |
//calculate the max cutoff |
347 |
> |
maxCutoff = calcMaxCutOff(); |
348 |
|
|
349 |
+ |
checkCutOffs(); |
350 |
+ |
|
351 |
|
} |
352 |
|
|
353 |
|
|
354 |
+ |
double SimInfo::calcMaxCutOff(){ |
355 |
+ |
|
356 |
+ |
double ri[3], rj[3], rk[3]; |
357 |
+ |
double rij[3], rjk[3], rki[3]; |
358 |
+ |
double minDist; |
359 |
+ |
|
360 |
+ |
ri[0] = Hmat[0][0]; |
361 |
+ |
ri[1] = Hmat[1][0]; |
362 |
+ |
ri[2] = Hmat[2][0]; |
363 |
+ |
|
364 |
+ |
rj[0] = Hmat[0][1]; |
365 |
+ |
rj[1] = Hmat[1][1]; |
366 |
+ |
rj[2] = Hmat[2][1]; |
367 |
+ |
|
368 |
+ |
rk[0] = Hmat[0][2]; |
369 |
+ |
rk[1] = Hmat[1][2]; |
370 |
+ |
rk[2] = Hmat[2][2]; |
371 |
+ |
|
372 |
+ |
crossProduct3(ri,rj, rij); |
373 |
+ |
distXY = dotProduct3(rk,rij) / length3(rij); |
374 |
+ |
|
375 |
+ |
crossProduct3(rj,rk, rjk); |
376 |
+ |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
377 |
+ |
|
378 |
+ |
crossProduct3(rk,ri, rki); |
379 |
+ |
distZX = dotProduct3(rj,rki) / length3(rki); |
380 |
+ |
|
381 |
+ |
minDist = min(min(distXY, distYZ), distZX); |
382 |
+ |
return minDist/2; |
383 |
+ |
|
384 |
+ |
} |
385 |
+ |
|
386 |
|
void SimInfo::wrapVector( double thePos[3] ){ |
387 |
|
|
388 |
< |
int i, j, k; |
388 |
> |
int i; |
389 |
|
double scaled[3]; |
390 |
|
|
391 |
|
if( !orthoRhombic ){ |
392 |
|
// calc the scaled coordinates. |
393 |
+ |
|
394 |
+ |
|
395 |
+ |
matVecMul3(HmatInv, thePos, scaled); |
396 |
|
|
397 |
|
for(i=0; i<3; i++) |
293 |
– |
scaled[i] = |
294 |
– |
thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6]; |
295 |
– |
|
296 |
– |
// wrap the scaled coordinates |
297 |
– |
|
298 |
– |
for(i=0; i<3; i++) |
398 |
|
scaled[i] -= roundMe(scaled[i]); |
399 |
|
|
400 |
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
401 |
|
|
402 |
< |
for(i=0; i<3; i++) |
403 |
< |
thePos[i] = |
305 |
< |
scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6]; |
402 |
> |
matVecMul3(Hmat, scaled, thePos); |
403 |
> |
|
404 |
|
} |
405 |
|
else{ |
406 |
|
// calc the scaled coordinates. |
407 |
|
|
408 |
|
for(i=0; i<3; i++) |
409 |
< |
scaled[i] = thePos[i]*HmatI[i*4]; |
409 |
> |
scaled[i] = thePos[i]*HmatInv[i][i]; |
410 |
|
|
411 |
|
// wrap the scaled coordinates |
412 |
|
|
416 |
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
417 |
|
|
418 |
|
for(i=0; i<3; i++) |
419 |
< |
thePos[i] = scaled[i]*Hmat[i*4]; |
419 |
> |
thePos[i] = scaled[i]*Hmat[i][i]; |
420 |
|
} |
421 |
|
|
324 |
– |
|
422 |
|
} |
423 |
|
|
424 |
|
|
425 |
|
int SimInfo::getNDF(){ |
426 |
< |
int ndf_local, ndf; |
426 |
> |
int ndf_local; |
427 |
|
|
428 |
|
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
429 |
|
|
433 |
|
ndf = ndf_local; |
434 |
|
#endif |
435 |
|
|
436 |
< |
ndf = ndf - 3; |
436 |
> |
ndf = ndf - 3 - nZconstraints; |
437 |
|
|
438 |
|
return ndf; |
439 |
|
} |
440 |
|
|
441 |
|
int SimInfo::getNDFraw() { |
442 |
< |
int ndfRaw_local, ndfRaw; |
442 |
> |
int ndfRaw_local; |
443 |
|
|
444 |
|
// Raw degrees of freedom that we have to set |
445 |
|
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
452 |
|
|
453 |
|
return ndfRaw; |
454 |
|
} |
455 |
< |
|
455 |
> |
|
456 |
> |
int SimInfo::getNDFtranslational() { |
457 |
> |
int ndfTrans_local; |
458 |
> |
|
459 |
> |
ndfTrans_local = 3 * n_atoms - n_constraints; |
460 |
> |
|
461 |
> |
#ifdef IS_MPI |
462 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
463 |
> |
#else |
464 |
> |
ndfTrans = ndfTrans_local; |
465 |
> |
#endif |
466 |
> |
|
467 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
468 |
> |
|
469 |
> |
return ndfTrans; |
470 |
> |
} |
471 |
> |
|
472 |
|
void SimInfo::refreshSim(){ |
473 |
|
|
474 |
|
simtype fInfo; |
475 |
|
int isError; |
476 |
|
int n_global; |
477 |
|
int* excl; |
478 |
< |
|
366 |
< |
fInfo.rrf = 0.0; |
367 |
< |
fInfo.rt = 0.0; |
478 |
> |
|
479 |
|
fInfo.dielect = 0.0; |
480 |
|
|
370 |
– |
fInfo.rlist = rList; |
371 |
– |
fInfo.rcut = rCut; |
372 |
– |
|
481 |
|
if( useDipole ){ |
374 |
– |
fInfo.rrf = ecr; |
375 |
– |
fInfo.rt = ecr - est; |
482 |
|
if( useReactionField )fInfo.dielect = dielectric; |
483 |
|
} |
484 |
|
|
524 |
|
|
525 |
|
this->ndf = this->getNDF(); |
526 |
|
this->ndfRaw = this->getNDFraw(); |
527 |
+ |
this->ndfTrans = this->getNDFtranslational(); |
528 |
+ |
} |
529 |
|
|
530 |
+ |
|
531 |
+ |
void SimInfo::setRcut( double theRcut ){ |
532 |
+ |
|
533 |
+ |
rCut = theRcut; |
534 |
+ |
checkCutOffs(); |
535 |
|
} |
536 |
|
|
537 |
+ |
void SimInfo::setDefaultRcut( double theRcut ){ |
538 |
+ |
|
539 |
+ |
haveOrigRcut = 1; |
540 |
+ |
origRcut = theRcut; |
541 |
+ |
rCut = theRcut; |
542 |
+ |
|
543 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
544 |
+ |
|
545 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
546 |
+ |
} |
547 |
+ |
|
548 |
+ |
void SimInfo::setEcr( double theEcr ){ |
549 |
+ |
|
550 |
+ |
ecr = theEcr; |
551 |
+ |
checkCutOffs(); |
552 |
+ |
} |
553 |
+ |
|
554 |
+ |
void SimInfo::setDefaultEcr( double theEcr ){ |
555 |
+ |
|
556 |
+ |
haveOrigEcr = 1; |
557 |
+ |
origEcr = theEcr; |
558 |
+ |
|
559 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
560 |
+ |
|
561 |
+ |
ecr = theEcr; |
562 |
+ |
|
563 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
564 |
+ |
} |
565 |
+ |
|
566 |
+ |
void SimInfo::setEcr( double theEcr, double theEst ){ |
567 |
+ |
|
568 |
+ |
est = theEst; |
569 |
+ |
setEcr( theEcr ); |
570 |
+ |
} |
571 |
+ |
|
572 |
+ |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
573 |
+ |
|
574 |
+ |
est = theEst; |
575 |
+ |
setDefaultEcr( theEcr ); |
576 |
+ |
} |
577 |
+ |
|
578 |
+ |
|
579 |
+ |
void SimInfo::checkCutOffs( void ){ |
580 |
+ |
|
581 |
+ |
int cutChanged = 0; |
582 |
+ |
|
583 |
+ |
if( boxIsInit ){ |
584 |
+ |
|
585 |
+ |
//we need to check cutOffs against the box |
586 |
+ |
|
587 |
+ |
//detect the change of rCut |
588 |
+ |
if(( maxCutoff > rCut )&&(usePBC)){ |
589 |
+ |
if( rCut < origRcut ){ |
590 |
+ |
rCut = origRcut; |
591 |
+ |
|
592 |
+ |
if (rCut > maxCutoff) |
593 |
+ |
rCut = maxCutoff; |
594 |
+ |
|
595 |
+ |
sprintf( painCave.errMsg, |
596 |
+ |
"New Box size is setting the long range cutoff radius " |
597 |
+ |
"to %lf at time %lf\n", |
598 |
+ |
rCut, currentTime ); |
599 |
+ |
painCave.isFatal = 0; |
600 |
+ |
simError(); |
601 |
+ |
} |
602 |
+ |
} |
603 |
+ |
else if ((rCut > maxCutoff)&&(usePBC)) { |
604 |
+ |
sprintf( painCave.errMsg, |
605 |
+ |
"New Box size is setting the long range cutoff radius " |
606 |
+ |
"to %lf at time %lf\n", |
607 |
+ |
maxCutoff, currentTime ); |
608 |
+ |
painCave.isFatal = 0; |
609 |
+ |
simError(); |
610 |
+ |
rCut = maxCutoff; |
611 |
+ |
} |
612 |
+ |
|
613 |
+ |
|
614 |
+ |
//detect the change of ecr |
615 |
+ |
if( maxCutoff > ecr ){ |
616 |
+ |
if( ecr < origEcr ){ |
617 |
+ |
ecr = origEcr; |
618 |
+ |
if (ecr > maxCutoff) ecr = maxCutoff; |
619 |
+ |
|
620 |
+ |
sprintf( painCave.errMsg, |
621 |
+ |
"New Box size is setting the electrostaticCutoffRadius " |
622 |
+ |
"to %lf at time %lf\n", |
623 |
+ |
ecr, currentTime ); |
624 |
+ |
painCave.isFatal = 0; |
625 |
+ |
simError(); |
626 |
+ |
} |
627 |
+ |
} |
628 |
+ |
else if( ecr > maxCutoff){ |
629 |
+ |
sprintf( painCave.errMsg, |
630 |
+ |
"New Box size is setting the electrostaticCutoffRadius " |
631 |
+ |
"to %lf at time %lf\n", |
632 |
+ |
maxCutoff, currentTime ); |
633 |
+ |
painCave.isFatal = 0; |
634 |
+ |
simError(); |
635 |
+ |
ecr = maxCutoff; |
636 |
+ |
} |
637 |
+ |
|
638 |
+ |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
639 |
+ |
|
640 |
+ |
// rlist is the 1.0 plus max( rcut, ecr ) |
641 |
+ |
|
642 |
+ |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
643 |
+ |
|
644 |
+ |
if( cutChanged ){ |
645 |
+ |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
646 |
+ |
} |
647 |
+ |
|
648 |
+ |
oldEcr = ecr; |
649 |
+ |
oldRcut = rCut; |
650 |
+ |
|
651 |
+ |
} else { |
652 |
+ |
// initialize this stuff before using it, OK? |
653 |
+ |
sprintf( painCave.errMsg, |
654 |
+ |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
655 |
+ |
painCave.isFatal = 1; |
656 |
+ |
simError(); |
657 |
+ |
} |
658 |
+ |
|
659 |
+ |
} |
660 |
+ |
|
661 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
662 |
+ |
|
663 |
+ |
map<string, GenericData*>::iterator result; |
664 |
+ |
result = properties.find(prop->getID()); |
665 |
+ |
|
666 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
667 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
668 |
+ |
|
669 |
+ |
if(result != properties.end()){ |
670 |
+ |
|
671 |
+ |
delete (*result).second; |
672 |
+ |
(*result).second = prop; |
673 |
+ |
|
674 |
+ |
} |
675 |
+ |
else{ |
676 |
+ |
|
677 |
+ |
properties[prop->getID()] = prop; |
678 |
+ |
|
679 |
+ |
} |
680 |
+ |
|
681 |
+ |
} |
682 |
+ |
|
683 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
684 |
+ |
|
685 |
+ |
map<string, GenericData*>::iterator result; |
686 |
+ |
|
687 |
+ |
//string lowerCaseName = (); |
688 |
+ |
|
689 |
+ |
result = properties.find(propName); |
690 |
+ |
|
691 |
+ |
if(result != properties.end()) |
692 |
+ |
return (*result).second; |
693 |
+ |
else |
694 |
+ |
return NULL; |
695 |
+ |
} |
696 |
+ |
|
697 |
+ |
vector<GenericData*> SimInfo::getProperties(){ |
698 |
+ |
|
699 |
+ |
vector<GenericData*> result; |
700 |
+ |
map<string, GenericData*>::iterator i; |
701 |
+ |
|
702 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
703 |
+ |
result.push_back((*i).second); |
704 |
+ |
|
705 |
+ |
return result; |
706 |
+ |
} |
707 |
+ |
|
708 |
+ |
double SimInfo::matTrace3(double m[3][3]){ |
709 |
+ |
double trace; |
710 |
+ |
trace = m[0][0] + m[1][1] + m[2][2]; |
711 |
+ |
|
712 |
+ |
return trace; |
713 |
+ |
} |