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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) if (j == 0)
bin_vector(compute->size_local_rows,compute->vector_local,1); bin_vector(compute->size_local_rows,compute->vector_local,1);
else 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); 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) if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/time compute does not calculate a vector"); error->all("Fix ave/time compute does not calculate a vector");
if (argindex[i] && modify->compute[icompute]->array_flag == 0) 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] && if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_array_cols) argindex[i] > modify->compute[icompute]->size_array_cols)
error->all("Fix ave/time compute array is accessed out-of-range"); 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]); int ifix = modify->find_fix(ids[i]);
if (ifix < 0) if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist"); 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"); error->all("Fix ave/time fix does not calculate a vector");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0) if (argindex[i] && modify->fix[ifix]->array_flag == 0)
error->all("Fix ave/time fix does not calculate a array"); error->all("Fix ave/time fix does not calculate an array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols) if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
error->all("Fix ave/time fix array is accessed out-of-range"); error->all("Fix ave/time fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq) if (nevery % modify->fix[ifix]->global_freq)
@ -689,9 +689,11 @@ void FixAveTime::invoke_vector(int ntimestep)
if (argindex[j] == 0) if (argindex[j] == 0)
for (i = 0; i < nrows; i++) for (i = 0; i < nrows; i++)
column[i] = fix->compute_vector(i); column[i] = fix->compute_vector(i);
else else {
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++) 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 // 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"); omega = memory->create_2d_double_array(nbody,3,"rigid:omega");
torque = memory->create_2d_double_array(nbody,3,"rigid:torque"); torque = memory->create_2d_double_array(nbody,3,"rigid:torque");
quat = memory->create_2d_double_array(nbody,4,"rigid:quat"); 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"); fflag = memory->create_2d_double_array(nbody,3,"rigid:fflag");
tflag = memory->create_2d_double_array(nbody,3,"rigid:tflag"); 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; array_flag = 1;
size_array_rows = nbody; size_array_rows = nbody;
size_array_cols = 12; size_array_cols = 15;
global_freq = 1; global_freq = 1;
extarray = 0; 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 // set here, so image value will persist from run to run
for (ibody = 0; ibody < nbody; ibody++) 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 // bitmasks for properties of extended particles
@ -404,7 +404,7 @@ FixRigid::~FixRigid()
memory->destroy_2d_double_array(omega); memory->destroy_2d_double_array(omega);
memory->destroy_2d_double_array(torque); memory->destroy_2d_double_array(torque);
memory->destroy_2d_double_array(quat); memory->destroy_2d_double_array(quat);
memory->sfree(image); memory->sfree(imagebody);
memory->destroy_2d_double_array(fflag); memory->destroy_2d_double_array(fflag);
memory->destroy_2d_double_array(tflag); 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 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 if don't do this, then atoms of a body which drifts far away
from a triclinic box will be remapped back into box 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() void FixRigid::pre_neighbor()
@ -1391,19 +1392,19 @@ void FixRigid::pre_neighbor()
int original,oldimage,newimage; int original,oldimage,newimage;
for (int ibody = 0; ibody < nbody; ibody++) { for (int ibody = 0; ibody < nbody; ibody++) {
original = image[ibody]; original = imagebody[ibody];
domain->remap(xcm[ibody],image[ibody]); domain->remap(xcm[ibody],imagebody[ibody]);
if (original == image[ibody]) remapflag[ibody][3] = 0; if (original == imagebody[ibody]) remapflag[ibody][3] = 0;
else { else {
oldimage = original & 1023; oldimage = original & 1023;
newimage = image[ibody] & 1023; newimage = imagebody[ibody] & 1023;
remapflag[ibody][0] = newimage - oldimage; remapflag[ibody][0] = newimage - oldimage;
oldimage = (original >> 10) & 1023; oldimage = (original >> 10) & 1023;
newimage = (image[ibody] >> 10) & 1023; newimage = (imagebody[ibody] >> 10) & 1023;
remapflag[ibody][1] = newimage - oldimage; remapflag[ibody][1] = newimage - oldimage;
oldimage = original >> 20; oldimage = original >> 20;
newimage = image[ibody] >> 20; newimage = imagebody[ibody] >> 20;
remapflag[ibody][2] = newimage - oldimage; remapflag[ibody][2] = newimage - oldimage;
remapflag[ibody][3] = 1; 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 // 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 nlocal = atom->nlocal;
int ibody,idim,otherdims; int ibody,idim,otherdims;
@ -1422,25 +1423,25 @@ void FixRigid::pre_neighbor()
ibody = body[i]; ibody = body[i];
if (remapflag[ibody][0]) { if (remapflag[ibody][0]) {
idim = atomimage[i] & 1023; idim = image[i] & 1023;
otherdims = atomimage[i] ^ idim; otherdims = image[i] ^ idim;
idim -= remapflag[ibody][0]; idim -= remapflag[ibody][0];
idim &= 1023; idim &= 1023;
atomimage[i] = otherdims | idim; image[i] = otherdims | idim;
} }
if (remapflag[ibody][1]) { if (remapflag[ibody][1]) {
idim = (atomimage[i] >> 10) & 1023; idim = (image[i] >> 10) & 1023;
otherdims = atomimage[i] ^ (idim << 10); otherdims = image[i] ^ (idim << 10);
idim -= remapflag[ibody][1]; idim -= remapflag[ibody][1];
idim &= 1023; idim &= 1023;
atomimage[i] = otherdims | (idim << 10); image[i] = otherdims | (idim << 10);
} }
if (remapflag[ibody][2]) { if (remapflag[ibody][2]) {
idim = atomimage[i] >> 20; idim = image[i] >> 20;
otherdims = atomimage[i] ^ (idim << 20); otherdims = image[i] ^ (idim << 20);
idim -= remapflag[ibody][2]; idim -= remapflag[ibody][2];
idim &= 1023; 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 return attributes of a rigid body
12 values per body 15 values per body
xcm = 1,2,3; vcm = 4,5,6; fcm = 7,8,9; torque = 10,11,12 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) double FixRigid::compute_array(int i, int j)
{ {
if (j <= 3) return xcm[i][j]; if (j < 3) return xcm[i][j];
if (j <= 6) return vcm[i][j-3]; if (j < 6) return vcm[i][j-3];
if (j <= 9) return fcm[i][j-6]; if (j < 9) return fcm[i][j-6];
return torque[i][j-9]; 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 **omega; // angular velocity of each in space coords
double **torque; // torque on each rigid body in space coords double **torque; // torque on each rigid body in space coords
double **quat; // quaternion of each rigid body 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 **fflag; // flag for on/off of center-of-mass force
double **tflag; // flag for on/off of center-of-mass torque double **tflag; // flag for on/off of center-of-mass torque