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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13008 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-01-30 18:51:56 +00:00
parent 18b5c363c2
commit e1cd500a21
7 changed files with 45 additions and 26 deletions
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1
src/compute.cpp
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@ -68,6 +68,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
scalar_flag = vector_flag = array_flag = 0;
peratom_flag = local_flag = 0;
size_vector_variable = size_array_rows_variable = 0;
tempflag = pressflag = peflag = 0;
pressatomflag = peatomflag = 0;

2
src/compute.h
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@ -39,6 +39,8 @@ class Compute : protected Pointers {
int size_vector; // length of global vector
int size_array_rows; // rows in global array
int size_array_cols; // columns in global array
int size_vector_variable; // 1 if vec length is unknown in advance
int size_array_rows_variable; // 1 if array rows is unknown in advance
int peratom_flag; // 0/1 if compute_peratom() function exists
int size_peratom_cols; // 0 = vector, N = columns in peratom array

2
src/domain.cpp
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@ -471,7 +471,7 @@ void Domain::reset_box()
MAX is important since coord - prd < lo can happen when coord = hi
if fix deform, remap velocity of fix group atoms by box edge velocities
for triclinic, atoms must be in lamda coords (0-1) before pbc is called
image = 10 bits for each dimension
image = 10 or 20 bits for each dimension depending on sizeof(imageint)
increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */

2
src/fix.cpp
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@ -69,7 +69,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
scalar_flag = vector_flag = array_flag = 0;
peratom_flag = local_flag = 0;
size_array_rows_variable = 0;
size_vector_variable = size_array_rows_variable = 0;
comm_forward = comm_reverse = comm_border = 0;
restart_reset = 0;

3
src/fix.h
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@ -57,7 +57,8 @@ class Fix : protected Pointers {
int size_vector; // length of global vector
int size_array_rows; // rows in global array
int size_array_cols; // columns in global array
int size_array_rows_variable; // 1 if row count is unknown in advance
int size_vector_variable; // 1 if vec length is unknown in advance
int size_array_rows_variable; // 1 if array rows is unknown in advance
int global_freq; // frequency s/v data is available at
int peratom_flag; // 0/1 if per-atom data is stored

27
src/thermo.cpp
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@ -860,14 +860,17 @@ void Thermo::parse_fields(char *str)
if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
if (modify->compute[n]->vector_flag == 0)
error->all(FLERR,"Thermo compute does not compute vector");
if (argindex1[nfield] > modify->compute[n]->size_vector)
if (argindex1[nfield] > modify->compute[n]->size_vector &&
modify->compute[n]->size_vector_variable == 0)
error->all(FLERR,"Thermo compute vector is accessed out-of-range");
}
if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
if (modify->compute[n]->array_flag == 0)
error->all(FLERR,"Thermo compute does not compute array");
if (argindex1[nfield] > modify->compute[n]->size_array_rows ||
argindex2[nfield] > modify->compute[n]->size_array_cols)
if (argindex1[nfield] > modify->compute[n]->size_array_rows &&
modify->compute[n]->size_array_rows_variable == 0)
error->all(FLERR,"Thermo compute array is accessed out-of-range");
if (argindex2[nfield] > modify->compute[n]->size_array_cols)
error->all(FLERR,"Thermo compute array is accessed out-of-range");
}
@ -887,16 +890,16 @@ void Thermo::parse_fields(char *str)
if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
if (modify->fix[n]->vector_flag == 0)
error->all(FLERR,"Thermo fix does not compute vector");
if (argindex1[nfield] > modify->fix[n]->size_vector)
if (argindex1[nfield] > modify->fix[n]->size_vector &&
modify->fix[n]->size_vector_variable == 0)
error->all(FLERR,"Thermo fix vector is accessed out-of-range");
}
if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
if (modify->fix[n]->array_flag == 0)
error->all(FLERR,"Thermo fix does not compute array");
if (argindex1[nfield] > modify->fix[n]->size_array_rows) {
if (modify->fix[n]->size_array_rows_variable == 0)
if (argindex1[nfield] > modify->fix[n]->size_array_rows &&
modify->fix[n]->size_array_rows_variable == 0)
error->all(FLERR,"Thermo fix array is accessed out-of-range");
}
if (argindex2[nfield] > modify->fix[n]->size_array_cols)
error->all(FLERR,"Thermo fix array is accessed out-of-range");
}
@ -1422,18 +1425,24 @@ void Thermo::compute_compute()
int m = field2index[ifield];
Compute *compute = computes[m];
// check for out-of-range access if vector/array is variable length
if (compute_which[m] == SCALAR) {
dvalue = compute->scalar;
if (normflag && compute->extscalar) dvalue /= natoms;
} else if (compute_which[m] == VECTOR) {
dvalue = compute->vector[argindex1[ifield]-1];
if (compute->size_vector_variable && argindex1[ifield] >
compute->size_vector) dvalue = 0.0;
else dvalue = compute->vector[argindex1[ifield]-1];
if (normflag) {
if (compute->extvector == 0) return;
else if (compute->extvector == 1) dvalue /= natoms;
else if (compute->extlist[argindex1[ifield]-1]) dvalue /= natoms;
}
} else {
dvalue = compute->array[argindex1[ifield]-1][argindex2[ifield]-1];
if (compute->size_array_rows_variable && argindex1[ifield] >
compute->size_array_rows) dvalue = 0.0;
else dvalue = compute->array[argindex1[ifield]-1][argindex2[ifield]-1];
if (normflag && compute->extarray) dvalue /= natoms;
}
}

26
src/variable.cpp
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@ -1081,7 +1081,8 @@ double Variable::evaluate(char *str, Tree **tree)
} else if (nbracket == 1 && compute->vector_flag) {
if (index1 > compute->size_vector)
if (index1 > compute->size_vector &&
compute->size_vector_variable == 0)
error->all(FLERR,"Variable formula compute vector "
"is accessed out-of-range");
if (update->whichflag == 0) {
@ -1093,7 +1094,9 @@ double Variable::evaluate(char *str, Tree **tree)
compute->invoked_flag |= INVOKED_VECTOR;
}
value1 = compute->vector[index1-1];
if (compute->size_vector_variable &&
index1 > compute->size_vector) value1 = 0.0;
else value1 = compute->vector[index1-1];
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@ -1107,7 +1110,8 @@ double Variable::evaluate(char *str, Tree **tree)
} else if (nbracket == 2 && compute->array_flag) {
if (index1 > compute->size_array_rows)
if (index1 > compute->size_array_rows &&
compute->size_array_rows_variable == 0)
error->all(FLERR,"Variable formula compute array "
"is accessed out-of-range");
if (index2 > compute->size_array_cols)
@ -1122,7 +1126,9 @@ double Variable::evaluate(char *str, Tree **tree)
compute->invoked_flag |= INVOKED_ARRAY;
}
value1 = compute->array[index1-1][index2-1];
if (compute->size_array_rows_variable &&
index1 > compute->size_array_rows) value1 = 0.0;
else value1 = compute->array[index1-1][index2-1];
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@ -1295,9 +1301,10 @@ double Variable::evaluate(char *str, Tree **tree)
} else if (nbracket == 1 && fix->vector_flag) {
if (index1 > fix->size_vector)
error->all(FLERR,
"Variable formula fix vector is accessed out-of-range");
if (index1 > fix->size_vector &&
fix->size_vector_variable == 0)
error->all(FLERR,"Variable formula fix vector is "
"accessed out-of-range");
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
error->all(FLERR,"Fix in variable not computed at compatible time");
@ -1315,11 +1322,10 @@ double Variable::evaluate(char *str, Tree **tree)
} else if (nbracket == 2 && fix->array_flag) {
if (index1 > fix->size_array_rows) {
if (fix->size_array_rows_variable == 0)
if (index1 > fix->size_array_rows &&
fix->size_array_rows_variable == 0)
error->all(FLERR,
"Variable formula fix array is accessed out-of-range");
}
if (index2 > fix->size_array_cols)
error->all(FLERR,
"Variable formula fix array is accessed out-of-range");