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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3512 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-12-09 21:12:49 +00:00
parent 41f61f38c7
commit 8b6877e6d0
21 changed files with 885 additions and 363 deletions
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173
src/thermo.cpp
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@ -53,7 +53,11 @@ using namespace LAMMPS_NS;
enum{IGNORE,WARN,ERROR}; // same as write_restart.cpp
enum{ONELINE,MULTILINE};
enum{INT,FLOAT};
enum{DUMMY0,INVOKED_SCALAR,INVOKED_VECTOR,DUMMMY3,INVOKED_PERATOM};
enum{SCALAR,VECTOR,ARRAY};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
#define MAXLINE 1024
#define DELTA 8
@ -271,16 +275,21 @@ void Thermo::compute(int flag)
// which = 0 is global scalar, which = 1 is global vector
for (i = 0; i < ncompute; i++)
if (compute_which[i] == 0) {
if (compute_which[i] == SCALAR) {
if (!(computes[i]->invoked_flag & INVOKED_SCALAR)) {
computes[i]->compute_scalar();
computes[i]->invoked_flag |= INVOKED_SCALAR;
}
} else {
} else if (compute_which[i] == VECTOR) {
if (!(computes[i]->invoked_flag & INVOKED_VECTOR)) {
computes[i]->compute_vector();
computes[i]->invoked_flag |= INVOKED_VECTOR;
}
} else if (compute_which[i] == ARRAY) {
if (!(computes[i]->invoked_flag & INVOKED_ARRAY)) {
computes[i]->compute_array();
computes[i]->invoked_flag |= INVOKED_ARRAY;
}
}
// if lineflag = MULTILINE, prepend step/cpu header line
@ -502,7 +511,8 @@ void Thermo::allocate()
for (int i = 0; i < n; i++) format_user[i] = NULL;
field2index = new int[n];
argindex = new int[n];
argindex1 = new int[n];
argindex2 = new int[n];
// factor of 3 is max number of computes a single field can add
@ -539,7 +549,8 @@ void Thermo::deallocate()
delete [] format_user;
delete [] field2index;
delete [] argindex;
delete [] argindex1;
delete [] argindex2;
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
delete [] id_compute;
@ -580,56 +591,56 @@ void Thermo::parse_fields(char *str)
} else if (strcmp(word,"temp") == 0) {
addfield("Temp",&Thermo::compute_temp,FLOAT);
index_temp = add_compute(id_temp,0);
index_temp = add_compute(id_temp,SCALAR);
} else if (strcmp(word,"press") == 0) {
addfield("Press",&Thermo::compute_press,FLOAT);
index_press_scalar = add_compute(id_press,0);
index_press_scalar = add_compute(id_press,SCALAR);
} else if (strcmp(word,"pe") == 0) {
addfield("PotEng",&Thermo::compute_pe,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"ke") == 0) {
addfield("KinEng",&Thermo::compute_ke,FLOAT);
index_temp = add_compute(id_temp,0);
index_temp = add_compute(id_temp,SCALAR);
} else if (strcmp(word,"etotal") == 0) {
addfield("TotEng",&Thermo::compute_etotal,FLOAT);
index_temp = add_compute(id_temp,0);
index_pe = add_compute(id_pe,0);
index_temp = add_compute(id_temp,SCALAR);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"enthalpy") == 0) {
addfield("Enthalpy",&Thermo::compute_enthalpy,FLOAT);
index_temp = add_compute(id_temp,0);
index_press_scalar = add_compute(id_press,0);
index_pe = add_compute(id_pe,0);
index_temp = add_compute(id_temp,SCALAR);
index_press_scalar = add_compute(id_press,SCALAR);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"evdwl") == 0) {
addfield("E_vdwl",&Thermo::compute_evdwl,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"ecoul") == 0) {
addfield("E_coul",&Thermo::compute_ecoul,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"epair") == 0) {
addfield("E_pair",&Thermo::compute_epair,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"ebond") == 0) {
addfield("E_bond",&Thermo::compute_ebond,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"eangle") == 0) {
addfield("E_angle",&Thermo::compute_eangle,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"edihed") == 0) {
addfield("E_dihed",&Thermo::compute_edihed,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"eimp") == 0) {
addfield("E_impro",&Thermo::compute_eimp,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"emol") == 0) {
addfield("E_mol",&Thermo::compute_emol,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"elong") == 0) {
addfield("E_long",&Thermo::compute_elong,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"etail") == 0) {
addfield("E_tail",&Thermo::compute_etail,FLOAT);
index_pe = add_compute(id_pe,0);
index_pe = add_compute(id_pe,SCALAR);
} else if (strcmp(word,"vol") == 0) {
addfield("Volume",&Thermo::compute_vol,FLOAT);
@ -662,25 +673,25 @@ void Thermo::parse_fields(char *str)
} else if (strcmp(word,"pxx") == 0) {
addfield("Pxx",&Thermo::compute_pxx,FLOAT);
index_press_vector = add_compute(id_press,1);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pyy") == 0) {
addfield("Pyy",&Thermo::compute_pyy,FLOAT);
index_press_vector = add_compute(id_press,1);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pzz") == 0) {
addfield("Pzz",&Thermo::compute_pzz,FLOAT);
index_press_vector = add_compute(id_press,1);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pxy") == 0) {
addfield("Pxy",&Thermo::compute_pxy,FLOAT);
index_press_vector = add_compute(id_press,1);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pxz") == 0) {
addfield("Pxz",&Thermo::compute_pxz,FLOAT);
index_press_vector = add_compute(id_press,1);
index_press_vector = add_compute(id_press,VECTOR);
} else if (strcmp(word,"pyz") == 0) {
addfield("Pyz",&Thermo::compute_pyz,FLOAT);
index_press_vector = add_compute(id_press,1);
index_press_vector = add_compute(id_press,VECTOR);
// compute value = c_ID, fix value = f_ID, variable value = v_ID
// if no trailing [], then arg is set to 0, else arg is between []
// count trailing [] and store int arguments
// copy = at most 8 chars of ID to pass to addfield
} else if ((strncmp(word,"c_",2) == 0) || (strncmp(word,"f_",2) == 0) ||
@ -693,38 +704,66 @@ void Thermo::parse_fields(char *str)
strncpy(copy,id,8);
copy[8] = '\0';
// parse zero or one or two trailing brackets from ID
// argindex1,argindex2 = int inside each bracket pair, 0 if no bracket
char *ptr = strchr(id,'[');
if (ptr) {
if (id[strlen(id)-1] != ']')
error->all("Invalid keyword in thermo_style custom command");
argindex[nfield] = atoi(ptr+1);
if (ptr == NULL) argindex1[nfield] = 0;
else {
*ptr = '\0';
} else argindex[nfield] = 0;
argindex1[nfield] = input->variable->int_between_brackets(ptr);
ptr++;
if (*ptr == '[') {
argindex2[nfield] = input->variable->int_between_brackets(ptr);
ptr++;
} else argindex2[nfield] = 0;
}
if (word[0] == 'c') {
n = modify->find_compute(id);
if (n < 0) error->all("Could not find thermo custom compute ID");
if (argindex[nfield] == 0 && modify->compute[n]->scalar_flag == 0)
error->all("Thermo compute ID does not compute scalar info");
if (argindex[nfield] > 0 && modify->compute[n]->vector_flag == 0)
error->all("Thermo compute ID does not compute vector info");
if (argindex[nfield] > 0 &&
argindex[nfield] > modify->compute[n]->size_vector)
error->all("Thermo compute ID vector is not large enough");
if (argindex1[nfield] == 0 && modify->compute[n]->scalar_flag == 0)
error->all("Thermo compute does not compute scalar");
if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
if (modify->compute[n]->vector_flag == 0)
error->all("Thermo compute does not compute vector");
if (argindex1[nfield] > modify->compute[n]->size_vector)
error->all("Thermo compute vector is accessed out-of-range");
}
if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
if (modify->compute[n]->array_flag == 0)
error->all("Thermo compute does not compute array");
if (argindex1[nfield] > modify->compute[n]->size_array_rows ||
argindex2[nfield] > modify->compute[n]->size_array_cols)
error->all("Thermo compute array is accessed out-of-range");
}
field2index[nfield] = add_compute(id,MIN(argindex[nfield],1));
if (argindex1[nfield] == 0)
field2index[nfield] = add_compute(id,SCALAR);
else if (argindex2[nfield] == 0)
field2index[nfield] = add_compute(id,VECTOR);
else
field2index[nfield] = add_compute(id,ARRAY);
addfield(copy,&Thermo::compute_compute,FLOAT);
} else if (word[0] == 'f') {
n = modify->find_fix(id);
if (n < 0) error->all("Could not find thermo custom fix ID");
if (argindex[nfield] == 0 && modify->fix[n]->scalar_flag == 0)
error->all("Thermo fix ID does not compute scalar info");
if (argindex[nfield] > 0 && modify->fix[n]->vector_flag == 0)
error->all("Thermo fix ID does not compute vector info");
if (argindex[nfield] > 0 &&
argindex[nfield] > modify->fix[n]->size_vector)
error->all("Thermo fix ID vector is not large enough");
if (argindex1[nfield] == 0 && modify->fix[n]->scalar_flag == 0)
error->all("Thermo fix does not compute scalar");
if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
if (modify->fix[n]->vector_flag == 0)
error->all("Thermo fix does not compute vector");
if (argindex1[nfield] > modify->fix[n]->size_vector)
error->all("Thermo fix vector is accessed out-of-range");
}
if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
if (modify->fix[n]->array_flag == 0)
error->all("Thermo fix does not compute array");
if (argindex1[nfield] > modify->fix[n]->size_array_rows ||
argindex2[nfield] > modify->fix[n]->size_array_cols)
error->all("Thermo fix array is accessed out-of-range");
}
field2index[nfield] = add_fix(id);
addfield(copy,&Thermo::compute_fix,FLOAT);
@ -734,6 +773,8 @@ void Thermo::parse_fields(char *str)
if (n < 0) error->all("Could not find thermo custom variable name");
if (input->variable->equalstyle(n) == 0)
error->all("Thermo custom variable is not equal-style variable");
if (argindex1[nfield])
error->all("Thermo custom variable cannot be indexed");
field2index[nfield] = add_variable(id);
addfield(copy,&Thermo::compute_variable,FLOAT);
@ -1150,17 +1191,22 @@ int Thermo::evaluate_keyword(char *word, double *answer)
void Thermo::compute_compute()
{
Compute *compute = computes[field2index[ifield]];
if (argindex[ifield] == 0) {
int m = field2index[ifield];
Compute *compute = computes[m];
if (compute_which[m] == SCALAR) {
dvalue = compute->scalar;
if (normflag && compute->extscalar) dvalue /= natoms;
} else {
dvalue = compute->vector[argindex[ifield]-1];
} else if (compute_which[m] == VECTOR) {
dvalue = compute->vector[argindex1[ifield]-1];
if (normflag) {
if (compute->extvector == 0) return;
else if (compute->extvector == 1) dvalue /= natoms;
else if (compute->extlist[argindex[ifield]-1]) dvalue /= natoms;
else if (compute->extlist[argindex1[ifield]-1]) dvalue /= natoms;
}
} else {
dvalue = compute->array[argindex1[ifield]-1][argindex2[ifield]-1];
if (normflag && compute->extarray) dvalue /= natoms;
}
}
@ -1168,17 +1214,22 @@ void Thermo::compute_compute()
void Thermo::compute_fix()
{
Fix *fix = fixes[field2index[ifield]];
if (argindex[ifield] == 0) {
int m = field2index[ifield];
Fix *fix = fixes[m];
if (argindex1[ifield] == 0) {
dvalue = fix->compute_scalar();
if (normflag && fix->extscalar) dvalue /= natoms;
} else {
dvalue = fix->compute_vector(argindex[ifield]-1);
} else if (argindex2[ifield] == 0) {
dvalue = fix->compute_vector(argindex1[ifield]-1);
if (normflag) {
if (fix->extvector == 0) return;
else if (fix->extvector == 1) dvalue /= natoms;
else if (fix->extlist[argindex[ifield]-1]) dvalue /= natoms;
else if (fix->extlist[argindex1[ifield]-1]) dvalue /= natoms;
}
} else {
dvalue = fix->compute_array(argindex1[ifield]-1,argindex2[ifield]-1);
if (normflag && fix->extarray) dvalue /= natoms;
}
}