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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4995 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-10-07 15:03:00 +00:00
parent e20c035199
commit c696189dfc
4 changed files with 41 additions and 35 deletions
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2
src/fix_ave_histo.cpp
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@ -653,7 +653,7 @@ void FixAveHisto::end_of_step()
if (j == 0)
bin_vector(compute->size_local_rows,compute->vector_local,1);
else
bin_vector(compute->size_local_rows,&compute->array_local[0][j],
bin_vector(compute->size_local_rows,&compute->array_local[0][j-1],
compute->size_local_cols);
}

14
src/fix_ave_time.cpp
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@ -189,7 +189,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/time compute does not calculate a vector");
if (argindex[i] && modify->compute[icompute]->array_flag == 0)
error->all("Fix ave/time compute does not calculate a array");
error->all("Fix ave/time compute does not calculate an array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_array_cols)
error->all("Fix ave/time compute array is accessed out-of-range");
@ -211,10 +211,10 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/time fix does not calculate a vector");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/time fix does not calculate a array");
if (argindex[i] && modify->fix[ifix]->array_flag == 0)
error->all("Fix ave/time fix does not calculate an array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
error->all("Fix ave/time fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
@ -689,9 +689,11 @@ void FixAveTime::invoke_vector(int ntimestep)
if (argindex[j] == 0)
for (i = 0; i < nrows; i++)
column[i] = fix->compute_vector(i);
else
else {
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = fix->compute_array(i,argindex[j]);
column[i] = fix->compute_array(i,icol);
}
}
// add columns of values to array or just set directly if offcol is set

58
src/fix_rigid.cpp
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@ -192,7 +192,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
omega = memory->create_2d_double_array(nbody,3,"rigid:omega");
torque = memory->create_2d_double_array(nbody,3,"rigid:torque");
quat = memory->create_2d_double_array(nbody,4,"rigid:quat");
image = (int *) memory->smalloc(nbody*sizeof(int),"rigid:image");
imagebody = (int *) memory->smalloc(nbody*sizeof(int),"rigid:imagebody");
fflag = memory->create_2d_double_array(nbody,3,"rigid:fflag");
tflag = memory->create_2d_double_array(nbody,3,"rigid:tflag");
@ -204,7 +204,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
array_flag = 1;
size_array_rows = nbody;
size_array_cols = 12;
size_array_cols = 15;
global_freq = 1;
extarray = 0;
@ -349,7 +349,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
// set here, so image value will persist from run to run
for (ibody = 0; ibody < nbody; ibody++)
image[ibody] = (512 << 20) | (512 << 10) | 512;
imagebody[ibody] = (512 << 20) | (512 << 10) | 512;
// bitmasks for properties of extended particles
@ -404,7 +404,7 @@ FixRigid::~FixRigid()
memory->destroy_2d_double_array(omega);
memory->destroy_2d_double_array(torque);
memory->destroy_2d_double_array(quat);
memory->sfree(image);
memory->sfree(imagebody);
memory->destroy_2d_double_array(fflag);
memory->destroy_2d_double_array(tflag);
@ -1383,7 +1383,8 @@ void FixRigid::final_integrate_respa(int ilevel, int iloop)
due to 1st definition of rigid body or due to box flip
if don't do this, then atoms of a body which drifts far away
from a triclinic box will be remapped back into box
with huge displacements when the box tilt changes via set_x()
with huge displacements when the box tilt changes via set_x()
adjust image flag of body and image flags of all atoms in body
------------------------------------------------------------------------- */
void FixRigid::pre_neighbor()
@ -1391,19 +1392,19 @@ void FixRigid::pre_neighbor()
int original,oldimage,newimage;
for (int ibody = 0; ibody < nbody; ibody++) {
original = image[ibody];
domain->remap(xcm[ibody],image[ibody]);
original = imagebody[ibody];
domain->remap(xcm[ibody],imagebody[ibody]);
if (original == image[ibody]) remapflag[ibody][3] = 0;
if (original == imagebody[ibody]) remapflag[ibody][3] = 0;
else {
oldimage = original & 1023;
newimage = image[ibody] & 1023;
newimage = imagebody[ibody] & 1023;
remapflag[ibody][0] = newimage - oldimage;
oldimage = (original >> 10) & 1023;
newimage = (image[ibody] >> 10) & 1023;
newimage = (imagebody[ibody] >> 10) & 1023;
remapflag[ibody][1] = newimage - oldimage;
oldimage = original >> 20;
newimage = image[ibody] >> 20;
newimage = imagebody[ibody] >> 20;
remapflag[ibody][2] = newimage - oldimage;
remapflag[ibody][3] = 1;
}
@ -1411,7 +1412,7 @@ void FixRigid::pre_neighbor()
// adjust image flags of any atom in a rigid body whose xcm was remapped
int *atomimage = atom->image;
int *image = atom->image;
int nlocal = atom->nlocal;
int ibody,idim,otherdims;
@ -1422,25 +1423,25 @@ void FixRigid::pre_neighbor()
ibody = body[i];
if (remapflag[ibody][0]) {
idim = atomimage[i] & 1023;
otherdims = atomimage[i] ^ idim;
idim = image[i] & 1023;
otherdims = image[i] ^ idim;
idim -= remapflag[ibody][0];
idim &= 1023;
atomimage[i] = otherdims | idim;
image[i] = otherdims | idim;
}
if (remapflag[ibody][1]) {
idim = (atomimage[i] >> 10) & 1023;
otherdims = atomimage[i] ^ (idim << 10);
idim = (image[i] >> 10) & 1023;
otherdims = image[i] ^ (idim << 10);
idim -= remapflag[ibody][1];
idim &= 1023;
atomimage[i] = otherdims | (idim << 10);
image[i] = otherdims | (idim << 10);
}
if (remapflag[ibody][2]) {
idim = atomimage[i] >> 20;
otherdims = atomimage[i] ^ (idim << 20);
idim = image[i] >> 20;
otherdims = image[i] ^ (idim << 20);
idim -= remapflag[ibody][2];
idim &= 1023;
atomimage[i] = otherdims | (idim << 20);
image[i] = otherdims | (idim << 20);
}
}
}
@ -2264,14 +2265,17 @@ void FixRigid::reset_dt()
/* ----------------------------------------------------------------------
return attributes of a rigid body
12 values per body
xcm = 1,2,3; vcm = 4,5,6; fcm = 7,8,9; torque = 10,11,12
15 values per body
xcm = 0,1,2; vcm = 3,4,5; fcm = 6,7,8; torque = 9,10,11; image = 12,13,14
------------------------------------------------------------------------- */
double FixRigid::compute_array(int i, int j)
{
if (j <= 3) return xcm[i][j];
if (j <= 6) return vcm[i][j-3];
if (j <= 9) return fcm[i][j-6];
return torque[i][j-9];
if (j < 3) return xcm[i][j];
if (j < 6) return vcm[i][j-3];
if (j < 9) return fcm[i][j-6];
if (j < 12) return torque[i][j-9];
if (j == 12) return (imagebody[i] & 1023) - 512;
if (j == 13) (imagebody[i] >> 10 & 1023) - 512;
return (imagebody[i] >> 20) - 512;
}

2
src/fix_rigid.h
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@ -67,7 +67,7 @@ class FixRigid : public Fix {
double **omega; // angular velocity of each in space coords
double **torque; // torque on each rigid body in space coords
double **quat; // quaternion of each rigid body
int *image; // image flags of xcm of each rigid body
int *imagebody; // image flags of xcm of each rigid body
double **fflag; // flag for on/off of center-of-mass force
double **tflag; // flag for on/off of center-of-mass torque