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Merge branch 'geoflow-merge' of https://github.com/Electrostatics/apbs-pdb2pqr into geoflow-merge

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Merging work done by @lizutah.
This commit is contained in:
kozlac
2015-12-22 15:39:55 -08:00
parent db0055d333 b5c4bf249c
commit 7f0e27cf80
3 changed files with 7 additions and 21 deletions
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2
externals/geoflow_c vendored

Submodule externals/geoflow_c updated: fae13d6dd5...b0c14f5e1a

14
src/generic/geoflowparm.c
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@@ -84,9 +84,6 @@ VPUBLIC Vrc_Codes GEOFLOWparm_ctor2(GEOFLOWparm *thee, GEOFLOWparm_CalcType type
thee->type = type;
thee->vdw = 0;
thee->etol = 1.0e-6;
// thee->dcel = 0.25;
// thee->pres = 0.008;
// thee->gama = 0.0001;
return VRC_SUCCESS;
}
@@ -135,9 +132,6 @@ VPUBLIC void GEOFLOWparm_copy(GEOFLOWparm *thee, GEOFLOWparm *parm) {
thee->vdw = parm->vdw;
thee->etol = parm->etol;
// thee->dcel = parm->dcel;
// thee->pres = parm->pres;
// thee->gama = parm->gama;
}
Vrc_Codes FUBAR(const char* name){
@@ -228,14 +222,6 @@ VPUBLIC Vrc_Codes GEOFLOWparm_parseToken(GEOFLOWparm *thee, char tok[VMAX_BUFSIZ
Vnm_print(0, "GEOFLOWparm_parseToken: trying %s...\n", tok);
// if (Vstring_strcasecmp(tok, "press") == 0) {
// return parseNonNeg(&(thee->pres), 0.008, &(thee->setpres), "pres", sock);
// } else if (Vstring_strcasecmp(tok, "gamma") == 0) {
// return parseNonNeg(&(thee->gama), 0.0001, &(thee->setgama), "gama", sock);
// } else if (Vstring_strcasecmp(tok, "grid") == 0) {
// return parseNonNeg(&(thee->dcel), 0.25, &(thee->setdcel), "dcel", sock);
// } else
if (Vstring_strcasecmp(tok, "vdwdisp") == 0) {
return GEOFLOWparm_parseVDW(thee, sock);
} else if(Vstring_strcasecmp(tok, "etol") == 0){

12
src/routines.c
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@@ -5109,21 +5109,21 @@ VPUBLIC int solveGeometricFlow( Valist* molecules[NOSH_MAXMOL],
struct GeometricFlowInput geoflowIn = getGeometricFlowParams();
// change any of the parameters you want...
geoflowIn.m_boundaryCondition = MDH; // should be: pbeparm->bcfl
geoflowIn.m_grid = apolparm->grid[0];
geoflowIn.m_boundaryCondition = (int) pbeparm->bcfl ;
geoflowIn.m_grid[0] = apolparm->grid[0];
geoflowIn.m_grid[1] = apolparm->grid[1];
geoflowIn.m_grid[2] = apolparm->grid[2];
geoflowIn.m_gamma = apolparm->gamma;
geoflowIn.m_pdie = pbeparm->pdie ;
geoflowIn.m_sdie = pbeparm->sdie ;
geoflowIn.m_press = apolparm->press ;
geoflowIn.m_tol = parm->etol;
printf("etol TEST: %lf\n", parm->etol);
geoflowIn.m_bconc = apolparm->bconc ;
geoflowIn.m_vdwdispersion = parm->vdw;
printf("vdw TEST: %i\n", parm->vdw);
geoflowIn.m_etolSolvation = .01 ; // to be added
geoflowIn.m_etolSolvation = .01 ; // to be added?
// debug
//printGeometricFlowStruct( geoflowIn );
printGeometricFlowStruct( geoflowIn );
printf("num mols: %i\n", nosh->nmol);
struct GeometricFlowOutput geoflowOut =