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#include <cmath> |
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3 |
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#include "Atom.hpp" |
4 |
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#include "simError.h" |
5 |
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6 |
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void DirectionalAtom::zeroForces() { |
7 |
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if( hasCoords ){ |
8 |
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frc[offsetX] = 0.0; |
9 |
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frc[offsetY] = 0.0; |
10 |
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frc[offsetZ] = 0.0; |
11 |
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|
12 |
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trq[offsetX] = 0.0; |
13 |
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trq[offsetY] = 0.0; |
14 |
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trq[offsetZ] = 0.0; |
15 |
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} |
16 |
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else{ |
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|
18 |
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sprintf( painCave.errMsg, |
19 |
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"Attempt to zero frc and trq for atom %d before coords set.\n", |
20 |
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index ); |
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painCave.isFatal = 1; |
22 |
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simError(); |
23 |
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} |
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} |
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|
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double DirectionalAtom::getMu( void ) { |
27 |
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|
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if( hasCoords ){ |
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return mu[index]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to get Mu for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
37 |
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simError(); |
38 |
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} |
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return 0; |
40 |
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} |
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|
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void DirectionalAtom::setMu( double the_mu ) { |
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|
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if( hasCoords ){ |
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mu[index] = the_mu; |
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} |
47 |
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else{ |
48 |
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|
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sprintf( painCave.errMsg, |
50 |
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"Attempt to set Mu for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
53 |
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simError(); |
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} |
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} |
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|
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void DirectionalAtom::setA( double the_A[3][3] ){ |
8 |
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|
9 |
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Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
10 |
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Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
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Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
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|
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this->updateU(); |
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if( hasCoords ){ |
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Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
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Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
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Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
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|
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this->updateU(); |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to set Amat for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void DirectionalAtom::setI( double the_I[3][3] ){ |
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|
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double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
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|
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q0Sqr = the_q[0] * the_q[0]; |
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q1Sqr = the_q[1] * the_q[1]; |
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q2Sqr = the_q[2] * the_q[2]; |
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q3Sqr = the_q[3] * the_q[3]; |
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|
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if( hasCoords ){ |
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q0Sqr = the_q[0] * the_q[0]; |
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q1Sqr = the_q[1] * the_q[1]; |
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q2Sqr = the_q[2] * the_q[2]; |
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q3Sqr = the_q[3] * the_q[3]; |
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|
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|
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Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
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Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
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Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
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|
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Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
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Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
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Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
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|
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Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
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Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
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Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
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|
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this->updateU(); |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
111 |
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"Attempt to set Q for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
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Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
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Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
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|
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Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
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Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
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Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
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|
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Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
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Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
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Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
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|
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this->updateU(); |
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} |
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|
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void DirectionalAtom::getA( double the_A[3][3] ){ |
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|
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the_A[0][0] = Amat[Axx]; |
122 |
< |
the_A[0][1] = Amat[Axy]; |
123 |
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the_A[0][2] = Amat[Axz]; |
121 |
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if( hasCoords ){ |
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the_A[0][0] = Amat[Axx]; |
123 |
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the_A[0][1] = Amat[Axy]; |
124 |
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the_A[0][2] = Amat[Axz]; |
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|
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the_A[1][0] = Amat[Ayx]; |
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the_A[1][1] = Amat[Ayy]; |
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the_A[1][2] = Amat[Ayz]; |
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|
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the_A[2][0] = Amat[Azx]; |
131 |
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the_A[2][1] = Amat[Azy]; |
132 |
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the_A[2][2] = Amat[Azz]; |
133 |
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} |
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else{ |
135 |
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|
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sprintf( painCave.errMsg, |
137 |
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"Attempt to get Amat for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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the_A[1][0] = Amat[Ayx]; |
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the_A[1][1] = Amat[Ayy]; |
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the_A[1][2] = Amat[Ayz]; |
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|
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the_A[2][0] = Amat[Azx]; |
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the_A[2][1] = Amat[Azy]; |
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the_A[2][2] = Amat[Azz]; |
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} |
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|
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void DirectionalAtom::printAmatIndex( void ){ |
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|
147 |
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std::cerr << "Atom[" << index << "] index =>\n" |
148 |
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<< "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n" |
149 |
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<< "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n" |
150 |
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<< "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n"; |
147 |
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if( hasCoords ){ |
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std::cerr << "Atom[" << index << "] index =>\n" |
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<< "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n" |
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<< "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n" |
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<< "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n"; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
156 |
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"Attempt to print Amat indices for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
159 |
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simError(); |
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} |
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} |
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|
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|
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double t, s; |
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double ad1, ad2, ad3; |
177 |
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|
178 |
< |
t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0; |
87 |
< |
if( t > 0.0 ){ |
178 |
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if( hasCoords ){ |
179 |
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|
180 |
< |
s = 0.5 / sqrt( t ); |
181 |
< |
q[0] = 0.25 / s; |
91 |
< |
q[1] = (Amat[Ayz] - Amat[Azy]) * s; |
92 |
< |
q[2] = (Amat[Azx] - Amat[Axz]) * s; |
93 |
< |
q[3] = (Amat[Axy] - Amat[Ayx]) * s; |
94 |
< |
} |
95 |
< |
else{ |
96 |
< |
|
97 |
< |
ad1 = fabs( Amat[Axx] ); |
98 |
< |
ad2 = fabs( Amat[Ayy] ); |
99 |
< |
ad3 = fabs( Amat[Azz] ); |
100 |
< |
|
101 |
< |
if( ad1 >= ad2 && ad1 >= ad3 ){ |
180 |
> |
t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0; |
181 |
> |
if( t > 0.0 ){ |
182 |
|
|
183 |
< |
s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] ); |
184 |
< |
q[0] = (Amat[Ayz] + Amat[Azy]) / s; |
185 |
< |
q[1] = 0.5 / s; |
186 |
< |
q[2] = (Amat[Axy] + Amat[Ayx]) / s; |
187 |
< |
q[3] = (Amat[Axz] + Amat[Azx]) / s; |
183 |
> |
s = 0.5 / sqrt( t ); |
184 |
> |
q[0] = 0.25 / s; |
185 |
> |
q[1] = (Amat[Ayz] - Amat[Azy]) * s; |
186 |
> |
q[2] = (Amat[Azx] - Amat[Axz]) * s; |
187 |
> |
q[3] = (Amat[Axy] - Amat[Ayx]) * s; |
188 |
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} |
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else if( ad2 >= ad1 && ad2 >= ad3 ){ |
110 |
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|
111 |
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s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0; |
112 |
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q[0] = (Amat[Axz] + Amat[Azx]) / s; |
113 |
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q[1] = (Amat[Axy] + Amat[Ayx]) / s; |
114 |
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q[2] = 0.5 / s; |
115 |
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q[3] = (Amat[Ayz] + Amat[Azy]) / s; |
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} |
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else{ |
190 |
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|
191 |
< |
s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
192 |
< |
q[0] = (Amat[Axy] + Amat[Ayx]) / s; |
193 |
< |
q[1] = (Amat[Axz] + Amat[Azx]) / s; |
194 |
< |
q[2] = (Amat[Ayz] + Amat[Azy]) / s; |
195 |
< |
q[3] = 0.5 / s; |
191 |
> |
ad1 = fabs( Amat[Axx] ); |
192 |
> |
ad2 = fabs( Amat[Ayy] ); |
193 |
> |
ad3 = fabs( Amat[Azz] ); |
194 |
> |
|
195 |
> |
if( ad1 >= ad2 && ad1 >= ad3 ){ |
196 |
> |
|
197 |
> |
s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] ); |
198 |
> |
q[0] = (Amat[Ayz] + Amat[Azy]) / s; |
199 |
> |
q[1] = 0.5 / s; |
200 |
> |
q[2] = (Amat[Axy] + Amat[Ayx]) / s; |
201 |
> |
q[3] = (Amat[Axz] + Amat[Azx]) / s; |
202 |
> |
} |
203 |
> |
else if( ad2 >= ad1 && ad2 >= ad3 ){ |
204 |
> |
|
205 |
> |
s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0; |
206 |
> |
q[0] = (Amat[Axz] + Amat[Azx]) / s; |
207 |
> |
q[1] = (Amat[Axy] + Amat[Ayx]) / s; |
208 |
> |
q[2] = 0.5 / s; |
209 |
> |
q[3] = (Amat[Ayz] + Amat[Azy]) / s; |
210 |
> |
} |
211 |
> |
else{ |
212 |
> |
|
213 |
> |
s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
214 |
> |
q[0] = (Amat[Axy] + Amat[Ayx]) / s; |
215 |
> |
q[1] = (Amat[Axz] + Amat[Azx]) / s; |
216 |
> |
q[2] = (Amat[Ayz] + Amat[Azy]) / s; |
217 |
> |
q[3] = 0.5 / s; |
218 |
> |
} |
219 |
|
} |
220 |
|
} |
221 |
+ |
else{ |
222 |
+ |
|
223 |
+ |
sprintf( painCave.errMsg, |
224 |
+ |
"Attempt to get Q for atom %d before coords set.\n", |
225 |
+ |
index ); |
226 |
+ |
painCave.isFatal = 1; |
227 |
+ |
simError(); |
228 |
+ |
} |
229 |
|
} |
230 |
|
|
231 |
|
|
232 |
|
void DirectionalAtom::setEuler( double phi, double theta, double psi ){ |
233 |
|
|
234 |
< |
Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
235 |
< |
Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
236 |
< |
Amat[Axz] = sin(theta) * sin(psi); |
237 |
< |
|
238 |
< |
Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
239 |
< |
Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
240 |
< |
Amat[Ayz] = sin(theta) * cos(psi); |
241 |
< |
|
242 |
< |
Amat[Azx] = sin(phi) * sin(theta); |
243 |
< |
Amat[Azy] = -cos(phi) * sin(theta); |
244 |
< |
Amat[Azz] = cos(theta); |
245 |
< |
|
246 |
< |
this->updateU(); |
234 |
> |
if( hasCoords ){ |
235 |
> |
Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
236 |
> |
Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
237 |
> |
Amat[Axz] = sin(theta) * sin(psi); |
238 |
> |
|
239 |
> |
Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
240 |
> |
Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
241 |
> |
Amat[Ayz] = sin(theta) * cos(psi); |
242 |
> |
|
243 |
> |
Amat[Azx] = sin(phi) * sin(theta); |
244 |
> |
Amat[Azy] = -cos(phi) * sin(theta); |
245 |
> |
Amat[Azz] = cos(theta); |
246 |
> |
|
247 |
> |
this->updateU(); |
248 |
> |
} |
249 |
> |
else{ |
250 |
> |
|
251 |
> |
sprintf( painCave.errMsg, |
252 |
> |
"Attempt to set Euler angles for atom %d before coords set.\n", |
253 |
> |
index ); |
254 |
> |
painCave.isFatal = 1; |
255 |
> |
simError(); |
256 |
> |
} |
257 |
|
} |
258 |
|
|
259 |
|
|
261 |
|
|
262 |
|
double rl[3]; // the lab frame vector |
263 |
|
|
264 |
< |
rl[0] = r[0]; |
265 |
< |
rl[1] = r[1]; |
266 |
< |
rl[2] = r[2]; |
264 |
> |
if( hasCoords ){ |
265 |
> |
rl[0] = r[0]; |
266 |
> |
rl[1] = r[1]; |
267 |
> |
rl[2] = r[2]; |
268 |
> |
|
269 |
> |
r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
270 |
> |
r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
271 |
> |
r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
272 |
> |
} |
273 |
> |
else{ |
274 |
> |
|
275 |
> |
sprintf( painCave.errMsg, |
276 |
> |
"Attempt to convert lab2body for atom %d before coords set.\n", |
277 |
> |
index ); |
278 |
> |
painCave.isFatal = 1; |
279 |
> |
simError(); |
280 |
> |
} |
281 |
|
|
155 |
– |
r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
156 |
– |
r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
157 |
– |
r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
282 |
|
} |
283 |
|
|
284 |
|
void DirectionalAtom::body2Lab( double r[3] ){ |
285 |
|
|
286 |
|
double rb[3]; // the body frame vector |
287 |
|
|
288 |
< |
rb[0] = r[0]; |
289 |
< |
rb[1] = r[1]; |
290 |
< |
rb[2] = r[2]; |
291 |
< |
|
292 |
< |
r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
293 |
< |
r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
294 |
< |
r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
288 |
> |
if( hasCoords ){ |
289 |
> |
rb[0] = r[0]; |
290 |
> |
rb[1] = r[1]; |
291 |
> |
rb[2] = r[2]; |
292 |
> |
|
293 |
> |
r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
294 |
> |
r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
295 |
> |
r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
296 |
> |
} |
297 |
> |
else{ |
298 |
> |
|
299 |
> |
sprintf( painCave.errMsg, |
300 |
> |
"Attempt to convert body2lab for atom %d before coords set.\n", |
301 |
> |
index ); |
302 |
> |
painCave.isFatal = 1; |
303 |
> |
simError(); |
304 |
> |
} |
305 |
|
} |
306 |
|
|
307 |
|
void DirectionalAtom::updateU( void ){ |
308 |
|
|
309 |
< |
ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz); |
310 |
< |
ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz); |
311 |
< |
ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz); |
309 |
> |
if( hasCoords ){ |
310 |
> |
ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz); |
311 |
> |
ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz); |
312 |
> |
ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz); |
313 |
> |
} |
314 |
> |
else{ |
315 |
> |
|
316 |
> |
sprintf( painCave.errMsg, |
317 |
> |
"Attempt to updateU for atom %d before coords set.\n", |
318 |
> |
index ); |
319 |
> |
painCave.isFatal = 1; |
320 |
> |
simError(); |
321 |
> |
} |
322 |
|
} |
323 |
|
|
324 |
|
void DirectionalAtom::getJ( double theJ[3] ){ |
337 |
|
|
338 |
|
void DirectionalAtom::getTrq( double theT[3] ){ |
339 |
|
|
340 |
< |
theT[0] = trq[offsetX]; |
341 |
< |
theT[1] = trq[offsetY]; |
342 |
< |
theT[2] = trq[offsetZ]; |
340 |
> |
if( hasCoords ){ |
341 |
> |
theT[0] = trq[offsetX]; |
342 |
> |
theT[1] = trq[offsetY]; |
343 |
> |
theT[2] = trq[offsetZ]; |
344 |
> |
} |
345 |
> |
else{ |
346 |
> |
|
347 |
> |
sprintf( painCave.errMsg, |
348 |
> |
"Attempt to get Trq for atom %d before coords set.\n", |
349 |
> |
index ); |
350 |
> |
painCave.isFatal = 1; |
351 |
> |
simError(); |
352 |
> |
} |
353 |
|
} |
354 |
|
|
355 |
|
void DirectionalAtom::addTrq( double theT[3] ){ |
356 |
|
|
357 |
< |
trq[offsetX] += theT[0]; |
358 |
< |
trq[offsetY] += theT[1]; |
359 |
< |
trq[offsetZ] += theT[2]; |
357 |
> |
if( hasCoords ){ |
358 |
> |
trq[offsetX] += theT[0]; |
359 |
> |
trq[offsetY] += theT[1]; |
360 |
> |
trq[offsetZ] += theT[2]; |
361 |
> |
} |
362 |
> |
else{ |
363 |
> |
|
364 |
> |
sprintf( painCave.errMsg, |
365 |
> |
"Attempt to add Trq for atom %d before coords set.\n", |
366 |
> |
index ); |
367 |
> |
painCave.isFatal = 1; |
368 |
> |
simError(); |
369 |
> |
} |
370 |
|
} |
371 |
|
|
372 |
|
|