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correctly compute adjusted box lengths for triclinic boxes. code taken from topotools

This commit is contained in:
Axel Kohlmeyer 2018-02-19 14:06:26 +01:00
parent 7bd089aa6d
commit 54dc73c771
1 changed files with 15 additions and 9 deletions
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24
tools/msi2lmp/src/ReadCarFile.c
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@ -73,7 +73,6 @@ void ReadCarFile(void)
int skip; /* lines to skip at beginning of file */
double lowest, highest; /* temp coordinate finding variables */
double total_q;
double sq_c;
double cos_alpha; /* Added by SLTM Sept 13, 2010 */
double cos_gamma;
double sin_gamma;
@ -261,7 +260,7 @@ void ReadCarFile(void)
box[2][k] = 0.0;
}
} else {
sq_c = pbc[2]*pbc[2];
double ly,lz;
cos_alpha = cos(pbc[3]*PI_180);
cos_gamma = cos(pbc[5]*PI_180);
sin_gamma = sin(pbc[5]*PI_180);
@ -275,16 +274,23 @@ void ReadCarFile(void)
B = pbc[1];
C = pbc[2];
/* compute xy, xz, and yz */
box[2][0] = B * cos_gamma;
box[2][1] = C * cos_beta;
if (fabs(sin_gamma) > 0.0001)
box[2][2] = C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma;
else box[2][2] = 0.0;
box[0][0] = -0.5*A + center[0] + shift[0];
box[1][0] = 0.5*A + center[0] + shift[0];
box[0][1] = -0.5*B*sin_gamma + center[1] + shift[1];
box[1][1] = 0.5*B*sin_gamma + center[1] + shift[1];
box[0][2] = -0.5*sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma) + center[2] + shift[2];
box[1][2] = 0.5*sqrt(sq_c * sin_beta*sin_beta - C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma) + center[2] + shift[2];
box[2][0] = B * cos_gamma; /* This is xy SLTM */
box[2][1] = C * cos_beta; /* This is xz SLTM */
box[2][2] = C*(cos_alpha-cos_gamma*cos_beta)/sin_gamma; /* This is yz SLTM */
/* compute adjusted box length for y and z and apply */
ly = sqrt(B*B - box[2][0]*box[2][0]);
lz = sqrt(C*C - box[2][1]*box[2][1] - box[2][2]*box[2][2]);
box[0][1] = -0.5*ly + center[1] + shift[1];
box[1][1] = 0.5*ly + center[1] + shift[1];
box[0][2] = -0.5*lz + center[2] + shift[2];
box[1][2] = 0.5*lz + center[2] + shift[2];
}
}