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@13301 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2015-03-26 18:02:08 +00:00
parent 1f6a1f4ad4
commit 3a3462678e
4 changed files with 35 additions and 22 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
src/fix_ave_chunk.cpp
View File

@ -299,7 +299,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
// increment lock counter in compute chunk/atom
// only if nrepeat > 1 or ave = RUNNING/WINDOW,
// so that locking spans multiple timesteps
// set lock here for ave = RUN/WINDOW or in end_of_step() for nrepeat > 1
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
@ -309,10 +308,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix ave/chunk does not use chunk/atom compute");
if (nrepeat > 1 || ave == RUNNING || ave == WINDOW) cchunk->lockcount++;
if (ave == RUNNING || ave == WINDOW) {
nchunk = cchunk->setup_chunks();
cchunk->lock(this,update->ntimestep,-1);
}
lockforever = 0;
// print file comment lines
@ -523,7 +519,11 @@ void FixAveChunk::end_of_step()
// zero out arrays that accumulate over many samples, but not across epochs
// invoke setup_chunks() to determine current nchunk
// re-allocate per-chunk arrays if needed
// invoke lock() so nchunk cannot change until Nfreq epoch is over
// invoke lock() in two cases:
// if nrepeat > 1: so nchunk cannot change until Nfreq epoch is over,
// will be unlocked on last repeat of this Nfreq
// if ave = RUNNING/WINDOW and not yet locked:
// set forever, will be unlocked in fix destructor
// wrap setup_chunks in clearstep/addstep b/c it may invoke computes
// both nevery and nfreq are future steps,
// since call below to cchunk->ichunk()
@ -539,6 +539,10 @@ void FixAveChunk::end_of_step()
allocate();
if (nrepeat > 1 && ave == ONE)
cchunk->lock(this,ntimestep,ntimestep+(nrepeat-1)*nevery);
else if ((ave == RUNNING || ave == WINDOW) && !lockforever) {
cchunk->lock(this,update->ntimestep,-1);
lockforever = 1;
}
for (m = 0; m < nchunk; m++) {
count_many[m] = count_sum[m] = 0.0;
for (i = 0; i < nvalues; i++) values_many[m][i] = 0.0;

1
src/fix_ave_chunk.h
View File

@ -54,6 +54,7 @@ class FixAveChunk : public Fix {
int nchunk,maxchunk;
char *idchunk;
class ComputeChunkAtom *cchunk;
int lockforever;
long filepos;

39
src/fix_ave_time.cpp
View File

@ -276,9 +276,6 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
// enable locking of row count by this fix for computes of variable length
// only if nrepeat > 1 or ave = RUNNING/WINDOW,
// so that locking spans multiple timesteps
// trigger lock_length here for ave = RUN/WINDOW
// or in end_of_step() for nrepeat > 1,
// so that row count = number of chunks is set
if (any_variable_length &&
(nrepeat > 1 || ave == RUNNING || ave == WINDOW)) {
@ -286,11 +283,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (varlen[i]) {
int icompute = modify->find_compute(ids[i]);
modify->compute[icompute]->lock_enable();
if (ave == RUNNING || ave == WINDOW) {
modify->compute[icompute]->lock_length();
modify->compute[icompute]->lock(this,update->ntimestep,-1);
}
}
lockforever = 0;
}
// print file comment lines
@ -435,7 +429,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
}
// initializations
// set vector_total/array_total to zero since it accumulates
// set vector_total to zero since it accumulates
// array_total already zeroed in allocate_arrays
irepeat = 0;
iwindow = window_limit = 0;
@ -443,9 +438,6 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (mode == SCALAR)
for (int i = 0; i < nvalues; i++) vector_total[i] = 0.0;
else
for (int i = 0; i < nrows; i++)
for (int j = 0; j < nvalues; j++) array_total[i][j] = 0.0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
@ -718,16 +710,16 @@ void FixAveTime::invoke_vector(bigint ntimestep)
// zero out arrays that accumulate over many samples, but not across epochs
// invoke setup_chunks() to determine current nchunk
// re-allocate per-chunk arrays if needed
// then invoke lock() so nchunk cannot change until Nfreq epoch is over
// use final arg = -1 for infinite-time window
// invoke lock() in two cases:
// if nrepeat > 1: so nchunk cannot change until Nfreq epoch is over,
// will be unlocked on last repeat of this Nfreq
// if ave = RUNNING/WINDOW and not yet locked:
// set forever, will be unlocked in fix destructor
// wrap setup_chunks in clearstep/addstep b/c it may invoke computes
// both nevery and nfreq are future steps,
// since call below to cchunk->ichunk()
// does not re-invoke internal cchunk compute on this same step
// first sample within single Nfreq epoch
// zero if first step
if (irepeat == 0) {
if (any_variable_length) {
modify->clearstep_compute();
@ -743,13 +735,19 @@ void FixAveTime::invoke_vector(bigint ntimestep)
}
bigint ntimestep = update->ntimestep;
int lockforever_flag = 0;
for (i = 0; i < nvalues; i++) {
if (!varlen[i]) continue;
if (nrepeat > 1 && ave == ONE) {
Compute *compute = modify->compute[value2index[i]];
compute->lock(this,ntimestep,ntimestep+(nrepeat-1)*nevery);
} else if ((ave == RUNNING || ave == WINDOW) && !lockforever) {
Compute *compute = modify->compute[value2index[i]];
compute->lock(this,update->ntimestep,-1);
lockforever_flag = 1;
}
}
if (lockforever_flag) lockforever = 1;
}
for (i = 0; i < nrows; i++)
@ -894,6 +892,10 @@ void FixAveTime::invoke_vector(bigint ntimestep)
fprintf(fp,"\n");
}
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
}
}
}
@ -1107,6 +1109,11 @@ void FixAveTime::allocate_arrays()
memory->destroy(array_list);
memory->create(array_list,nwindow,nrows,nvalues,"ave/time:array_list");
}
// reinitialize regrown array_total since it accumulates
for (int i = 0; i < nrows; i++)
for (int j = 0; j < nvalues; j++) array_total[i][j] = 0.0;
}
/* ----------------------------------------------------------------------

1
src/fix_ave_time.h
View File

@ -48,6 +48,7 @@ class FixAveTime : public Fix {
int nrows;
int any_variable_length;
int all_variable_length;
int lockforever;
int ave,nwindow,startstep,mode;
int noff,overwrite;