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fix longstanding improper/OOP bug in msi2lmp

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This commit is contained in:
Axel Kohlmeyer
2013-07-11 23:53:23 +02:00
parent 8757924908
commit 1adad55790
2 changed files with 25 additions and 26 deletions
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2
tools/msi2lmp/src/Forcefield.h
View File

@ -6,7 +6,7 @@
* It defines the data structures used to store the force field in memory
*/
#define MAX_NO_MEMS 5
#define MAX_NO_MEMS 6
#define MAX_NO_PARAMS 8
struct FrcFieldData {

49
tools/msi2lmp/src/GetParameters.c
View File

@ -73,7 +73,7 @@ void GetParameters(int Forcefield)
if (k < 0) {
get_equivs(1,potential_types,equiv_types);
if (pflag > 2) printf("Using equivalences for VDW %s -> %s\n",
if (pflag > 2) printf(" Using equivalences for VDW %s -> %s\n",
potential_types[0],equiv_types[0]);
k = find_match(1,equiv_types,ff_vdw,&backwards);
@ -124,7 +124,7 @@ void GetParameters(int Forcefield)
get_equivs(2,potential_types,equiv_types);
if (pflag > 2) {
printf("Using equivalences for bond %s %s -> %s %s\n",
printf(" Using equivalences for bond %s %s -> %s %s\n",
potential_types[0],potential_types[1],
equiv_types[0],equiv_types[1]);
}
@ -149,7 +149,7 @@ void GetParameters(int Forcefield)
printf("\n Bond Types and Parameters\n");
for (i=0; i < no_bond_types; i++) {
for (j=0; j < 2; j++)
printf("%-3s",atomtypes[bondtypes[i].types[j]].potential);
printf(" %-3s",atomtypes[bondtypes[i].types[j]].potential);
for (j=0; j < 4; j++)
printf(" %8.4f",bondtypes[i].params[j]);
printf("\n");
@ -177,7 +177,7 @@ void GetParameters(int Forcefield)
if (k < 0) {
get_equivs(3,potential_types,equiv_types);
if (pflag > 2) {
printf("Using equivalences for angle %s %s %s -> %s %s %s\n",
printf(" Using equivalences for angle %s %s %s -> %s %s %s\n",
potential_types[0],potential_types[1],
potential_types[2],
equiv_types[0],equiv_types[1],
@ -201,7 +201,7 @@ void GetParameters(int Forcefield)
if (Forcefield > 1) {
get_equivs(3,potential_types,equiv_types);
if (pflag > 2) {
printf("Using equivalences for 3 body cross terms %s %s %s -> %s %s %s\n",
printf(" Using equivalences for 3 body cross terms %s %s %s -> %s %s %s\n",
potential_types[0],potential_types[1],potential_types[2],
equiv_types[0],equiv_types[1],equiv_types[2]);
}
@ -260,7 +260,7 @@ void GetParameters(int Forcefield)
printf("\n BondBond Types and Parameters\n");
for (i=0; i < no_angle_types; i++) {
for (j=0; j < 3; j++)
printf("%-3s",atomtypes[angletypes[i].types[j]].potential);
printf(" %-3s",atomtypes[angletypes[i].types[j]].potential);
for (j=0; j < 3; j++)
printf(" %8.4f",angletypes[i].bondbond_cross_term[j]);
printf("\n");
@ -268,7 +268,7 @@ void GetParameters(int Forcefield)
printf("\n BondAngle Types and Parameters\n");
for (i=0; i < no_angle_types; i++) {
for (j=0; j < 3; j++)
printf("%-3s",atomtypes[angletypes[i].types[j]].potential);
printf(" %-3s",atomtypes[angletypes[i].types[j]].potential);
for (j=0; j < 4; j++)
printf(" %8.4f",angletypes[i].bondangle_cross_term[j]);
printf("\n");
@ -302,7 +302,7 @@ void GetParameters(int Forcefield)
get_equivs(4,potential_types,equiv_types);
if (pflag > 2) {
printf("Using equivalences for dihedral %s %s %s %s -> %s %s %s %s\n",
printf(" Using equivalences for dihedral %s %s %s %s -> %s %s %s %s\n",
potential_types[0],potential_types[1],
potential_types[2],potential_types[3],
equiv_types[0],equiv_types[1],
@ -333,7 +333,7 @@ void GetParameters(int Forcefield)
else if (ff_tor.data[k].ff_param[2] == 180.0)
dihedraltypes[i].params[1] = -1.0;
else {
printf("Non planar phi0 for %s %s %s %s\n",
printf(" Non planar phi0 for %s %s %s %s\n",
potential_types[0],potential_types[1],
potential_types[2],potential_types[3]);
dihedraltypes[i].params[1] = 0.0;
@ -349,7 +349,7 @@ void GetParameters(int Forcefield)
if (Forcefield > 1) {
get_equivs(4,potential_types,equiv_types);
if (pflag > 2) {
printf("Using equivalences for linear 4 body cross terms %s %s %s %s -> %s %s %s %s\n",
printf(" Using equivalences for linear 4 body cross terms %s %s %s %s -> %s %s %s %s\n",
potential_types[0],potential_types[1],
potential_types[2],potential_types[3],
equiv_types[0],equiv_types[1],
@ -529,7 +529,7 @@ void GetParameters(int Forcefield)
printf("\n Dihedral Types and Parameters\n");
for (i=0; i < no_dihedral_types; i++) {
for (j=0; j < 4; j++)
printf("%-3s",atomtypes[dihedraltypes[i].types[j]].potential);
printf(" %-3s",atomtypes[dihedraltypes[i].types[j]].potential);
for (j=0; j < 6; j++)
printf(" %8.4f",dihedraltypes[i].params[j]);
printf("\n");
@ -540,7 +540,7 @@ void GetParameters(int Forcefield)
printf("\n EndBondDihedral Types and Parameters\n");
for (i=0; i < no_dihedral_types; i++) {
for (j=0; j < 4; j++)
printf("%-3s",atomtypes[dihedraltypes[i].types[j]].potential);
printf(" %-3s",atomtypes[dihedraltypes[i].types[j]].potential);
for (j=0; j < 8; j++)
printf(" %8.4f",dihedraltypes[i].endbonddihedral_cross_term[j]);
printf("\n");
@ -557,7 +557,7 @@ void GetParameters(int Forcefield)
printf("\n AngleDihedral Types and Parameters\n");
for (i=0; i < no_dihedral_types; i++) {
for (j=0; j < 4; j++)
printf("%-3s",atomtypes[dihedraltypes[i].types[j]].potential);
printf(" %-3s",atomtypes[dihedraltypes[i].types[j]].potential);
for (j=0; j < 8; j++)
printf(" %8.4f",dihedraltypes[i].angledihedral_cross_term[j]);
printf("\n");
@ -568,7 +568,7 @@ void GetParameters(int Forcefield)
for (j=0; j < 4; j++)
printf(" %-3s",atomtypes[dihedraltypes[i].types[j]].potential);
for (j=0; j < 3; j++)
printf("%8.4f",dihedraltypes[i].angleangledihedral_cross_term[j]);
printf(" %8.4f",dihedraltypes[i].angleangledihedral_cross_term[j]);
printf("\n");
}
@ -618,7 +618,7 @@ void GetParameters(int Forcefield)
get_equivs(5,potential_types,equiv_types);
if (pflag > 2) {
printf("Using equivalences for oop %s %s %s %s -> %s %s %s %s\n",
printf(" Using equivalences for oop %s %s %s %s -> %s %s %s %s\n",
potential_types[0],potential_types[1],
potential_types[2],potential_types[3],
equiv_types[0],equiv_types[1],
@ -638,7 +638,7 @@ void GetParameters(int Forcefield)
else if (ff_oop.data[k].ff_param[2] == 180.0)
ooptypes[i].params[1] = -1.0;
else {
printf("Non planar phi0 for %s %s %s %s\n",
printf(" Non planar phi0 for %s %s %s %s\n",
potential_types[0],potential_types[1],
potential_types[2],potential_types[3]);
ooptypes[i].params[1] = 0.0;
@ -658,7 +658,7 @@ void GetParameters(int Forcefield)
if (k < 0) {
get_equivs(5,potential_types,equiv_types);
if (pflag > 2) {
printf("Using equivalences for oop %s %s %s %s -> %s %s %s %s\n",
printf(" Using equivalences for oop %s %s %s %s -> %s %s %s %s\n",
potential_types[0],potential_types[1],
potential_types[2],potential_types[3],
equiv_types[0],equiv_types[1],
@ -682,7 +682,7 @@ void GetParameters(int Forcefield)
printf("\n OOP Types and Parameters\n");
for (i=0; i < no_oop_types; i++) {
for (j=0; j < 4; j++)
printf("%-3s",atomtypes[ooptypes[i].types[j]].potential);
printf(" %-3s",atomtypes[ooptypes[i].types[j]].potential);
for (j=0; j < 3; j++)
printf(" %8.4f",ooptypes[i].params[j]);
printf("\n");
@ -733,7 +733,7 @@ void GetParameters(int Forcefield)
if (k < 0) {
get_equivs(5,potential_types,equiv_types);
if (pflag > 2) {
printf("Using equivalences for angleangle %s %s %s %s -> %s %s %s %s\n",
printf(" Using equivalences for angleangle %s %s %s %s -> %s %s %s %s\n",
potential_types[0],potential_types[1],
potential_types[2],potential_types[3],
equiv_types[0],equiv_types[1],
@ -803,7 +803,7 @@ void GetParameters(int Forcefield)
printf("\n AngleAngle Types and Parameters\n");
for (i=0; i < no_oop_types; i++) {
for (j=0; j < 4; j++)
printf("%-3s",atomtypes[ooptypes[i].types[j]].potential);
printf(" %-3s",atomtypes[ooptypes[i].types[j]].potential);
for (j=0; j < 6; j++)
printf(" %8.4f",ooptypes[i].angleangle_params[j]);
printf("\n");
@ -1193,7 +1193,7 @@ double get_r0(int typei,int typej)
}
if (match == 0)
printf("Unable to find r0 for types %d %d\n",typei,typej);
printf(" Unable to find r0 for types %d %d\n",typei,typej);
return r;
}
@ -1279,13 +1279,12 @@ void get_equivs(int ic,char potential_types[][5],char equiv_types[][5])
for (i=0; i < 4; i++) {
k = find_equiv_type(potential_types[i]);
if (k > -1)
/* XXX: this leads to an out-of-bounds access.
the change below does not seem to make a difference.
strncpy(equiv_types[i],equivalence.data[k].ff_types[5],5); */
strncpy(equiv_types[i],equivalence.data[k].ff_types[4],5);
strncpy(equiv_types[i],equivalence.data[k].ff_types[5],5);
}
break;
default:
printf(" Requesting equivalences of unsupported type: %d\n",ic);
condexit(26);
break;
}
return;