ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12650 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-10-28 19:53:17 +00:00
parent 7cea65198f
commit 51a148df16
18 changed files with 632 additions and 274 deletions
Download Patch File Download Diff File Expand all files Collapse all files

40
lib/colvars/colvartypes.cpp
View File

@ -350,22 +350,22 @@ void colvarmodule::rotation::calc_optimal_rotation
// derivative of the S matrix
ds_1.reset();
ds_1[0][0] = cvm::rvector ( a2x, a2y, a2z);
ds_1[1][0] = cvm::rvector ( 0.0, a2z, -a2y);
ds_1[0][0].set( a2x, a2y, a2z);
ds_1[1][0].set( 0.0, a2z, -a2y);
ds_1[0][1] = ds_1[1][0];
ds_1[2][0] = cvm::rvector (-a2z, 0.0, a2x);
ds_1[2][0].set(-a2z, 0.0, a2x);
ds_1[0][2] = ds_1[2][0];
ds_1[3][0] = cvm::rvector ( a2y, -a2x, 0.0);
ds_1[3][0].set( a2y, -a2x, 0.0);
ds_1[0][3] = ds_1[3][0];
ds_1[1][1] = cvm::rvector ( a2x, -a2y, -a2z);
ds_1[2][1] = cvm::rvector ( a2y, a2x, 0.0);
ds_1[1][1].set( a2x, -a2y, -a2z);
ds_1[2][1].set( a2y, a2x, 0.0);
ds_1[1][2] = ds_1[2][1];
ds_1[3][1] = cvm::rvector ( a2z, 0.0, a2x);
ds_1[3][1].set( a2z, 0.0, a2x);
ds_1[1][3] = ds_1[3][1];
ds_1[2][2] = cvm::rvector (-a2x, a2y, -a2z);
ds_1[3][2] = cvm::rvector ( 0.0, a2z, a2y);
ds_1[2][2].set(-a2x, a2y, -a2z);
ds_1[3][2].set( 0.0, a2z, a2y);
ds_1[2][3] = ds_1[3][2];
ds_1[3][3] = cvm::rvector (-a2x, -a2y, a2z);
ds_1[3][3].set(-a2x, -a2y, a2z);
cvm::rvector &dl0_1 = dL0_1[ia];
vector1d<cvm::rvector, 4> &dq0_1 = dQ0_1[ia];
@ -404,22 +404,22 @@ void colvarmodule::rotation::calc_optimal_rotation
matrix2d<cvm::rvector, 4, 4> &ds_2 = dS_2[ia];
ds_2.reset();
ds_2[0][0] = cvm::rvector ( a1x, a1y, a1z);
ds_2[1][0] = cvm::rvector ( 0.0, -a1z, a1y);
ds_2[0][0].set( a1x, a1y, a1z);
ds_2[1][0].set( 0.0, -a1z, a1y);
ds_2[0][1] = ds_2[1][0];
ds_2[2][0] = cvm::rvector ( a1z, 0.0, -a1x);
ds_2[2][0].set( a1z, 0.0, -a1x);
ds_2[0][2] = ds_2[2][0];
ds_2[3][0] = cvm::rvector (-a1y, a1x, 0.0);
ds_2[3][0].set(-a1y, a1x, 0.0);
ds_2[0][3] = ds_2[3][0];
ds_2[1][1] = cvm::rvector ( a1x, -a1y, -a1z);
ds_2[2][1] = cvm::rvector ( a1y, a1x, 0.0);
ds_2[1][1].set( a1x, -a1y, -a1z);
ds_2[2][1].set( a1y, a1x, 0.0);
ds_2[1][2] = ds_2[2][1];
ds_2[3][1] = cvm::rvector ( a1z, 0.0, a1x);
ds_2[3][1].set( a1z, 0.0, a1x);
ds_2[1][3] = ds_2[3][1];
ds_2[2][2] = cvm::rvector (-a1x, a1y, -a1z);
ds_2[3][2] = cvm::rvector ( 0.0, a1z, a1y);
ds_2[2][2].set(-a1x, a1y, -a1z);
ds_2[3][2].set( 0.0, a1z, a1y);
ds_2[2][3] = ds_2[3][2];
ds_2[3][3] = cvm::rvector (-a1x, -a1y, a1z);
ds_2[3][3].set(-a1x, -a1y, a1z);
cvm::rvector &dl0_2 = dL0_2[ia];
vector1d<cvm::rvector, 4> &dq0_2 = dQ0_2[ia];