/dports/science/nwchem-data/nwchem-7.0.2-release/src/dplot/ |
H A D | get_charges.F | 30 Integer iAtom,jAtom,iCart 47 Do iAtom = 1, nAtom 48 Dst(iGrid,iAtom) = Sqrt( Dst(iGrid,iAtom) ) 54 Do iAtom = 1, nAtom 63 Write(*,'(10f12.6)')(Dst(iGrid,iAtom),iAtom=1,nAtom) 103 Write(*,'(5f10.5)')(Charge(iAtom),iAtom = 1, nAtom) 115 Do iAtom = 1, nAtom 116 Sum = Sum + Charge(iAtom)/Dst(iGrid,iAtom) 138 Do iAtom = 1, nAtom 179 Charge(iAtom)= BMt(iAtom) [all …]
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H A D | get_grid.F | 24 Integer i,iGrid,iX,iY,iZ,Const_M(3),Const_P(3),iAtom 51 Do iAtom = 1, nAtom 54 Dist = Dist + ( Grid(i,iGrid)-XYZ(i,iAtom) )**2 82 Do iAtom = 1, nAtom 85 Dist = Dist + ( Grid(i,iGrid)-XYZ(i,iAtom) )**2 120 Do iAtom = 1, nAtom 123 Dist = Dist + ( Grid(i,iGrid)-XYZ(i,iAtom) )**2 147 Do iAtom = 1, nAtom 150 Dist = Dist + ( Grid(i,iGrid)-XYZ(i,iAtom) )**2
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/dplot/ |
H A D | get_charges.F | 30 Integer iAtom,jAtom,iCart 47 Do iAtom = 1, nAtom 48 Dst(iGrid,iAtom) = Sqrt( Dst(iGrid,iAtom) ) 54 Do iAtom = 1, nAtom 63 Write(*,'(10f12.6)')(Dst(iGrid,iAtom),iAtom=1,nAtom) 103 Write(*,'(5f10.5)')(Charge(iAtom),iAtom = 1, nAtom) 115 Do iAtom = 1, nAtom 116 Sum = Sum + Charge(iAtom)/Dst(iGrid,iAtom) 138 Do iAtom = 1, nAtom 179 Charge(iAtom)= BMt(iAtom) [all …]
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H A D | get_grid.F | 24 Integer i,iGrid,iX,iY,iZ,Const_M(3),Const_P(3),iAtom 64 Do iAtom = 1, nAtom 67 Dist = Dist + ( Grid(i,iGrid)-XYZ(i,iAtom) )**2 95 Do iAtom = 1, nAtom 98 Dist = Dist + ( Grid(i,iGrid)-XYZ(i,iAtom) )**2 133 Do iAtom = 1, nAtom 136 Dist = Dist + ( Grid(i,iGrid)-XYZ(i,iAtom) )**2 160 Do iAtom = 1, nAtom 163 Dist = Dist + ( Grid(i,iGrid)-XYZ(i,iAtom) )**2
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/dimqm/ |
H A D | dimqm_f2d.F | 30 integer i, i3, i0, id, iAtom, iOrder 49 do iAtom = 1, nDIM 50 i0 = 3 * (iAtom - 1) 51 tempArr(i0+1,i) = fld(1,iAtom,i) 52 tempArr(i0+2,i) = fld(2,iAtom,i) 53 tempArr(i0+3,i) = fld(3,iAtom,i) 120 do iAtom = 1, nDIM 122 i0 = 3 * ( iAtom - 1 ) 124 muind(1,iAtom, i) = tempArr(i0+1,i) 128 muind(2,iAtom,i) = tempArr(i0+2,i) [all …]
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/dimqm/ |
H A D | dimqm_f2d.F | 30 integer i, i3, i0, id, iAtom, iOrder 49 do iAtom = 1, nDIM 50 i0 = 3 * (iAtom - 1) 51 tempArr(i0+1,i) = fld(1,iAtom,i) 52 tempArr(i0+2,i) = fld(2,iAtom,i) 53 tempArr(i0+3,i) = fld(3,iAtom,i) 120 do iAtom = 1, nDIM 122 i0 = 3 * ( iAtom - 1 ) 124 muind(1,iAtom, i) = tempArr(i0+1,i) 128 muind(2,iAtom,i) = tempArr(i0+2,i) [all …]
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/dports/science/dftbplus/dftbplus-19.1/prog/dftb+/lib_dftb/ |
H A D | sccinit.F90 | 308 do iAtom = 1, nAtom 309 nOrb = orb%nOrbAtom(iAtom) 347 do iAtom = 1, nAtom 364 do iAtom = 1, nAtom 365 nOrb = orb%nOrbAtom(iAtom) 367 qBlock(ii, ii ,iAtom, iSpin) = qq(ii ,iAtom, iSpin) 377 do iAtom = 1, nAtom 499 do iAtom = 1, nAtom 500 nOrb = orb%nOrbAtom(iAtom) 515 do iAtom = 1, nAtom [all …]
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H A D | spin.F90 | 68 integer :: nAtom, iAtom, iSpecies, iShell, iShell2, nSpin, iSpin local 80 do iAtom = 1, nAtom 81 iSpecies = species(iAtom) 84 shift(iShell, iAtom, iSpin) = shift(iShell, iAtom, iSpin) + & 85 & spinW(iShell, iShell2, iSpecies) * chargePerShell(iShell2, iAtom, iSpin)
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/quantum/ |
H A D | MopacSlaterReader.java | 218 createSphericalSlaterByType(iAtom, atomicNumber, "S", zeta, 1); in createMopacSlaters() 221 createSphericalSlaterByType(iAtom, atomicNumber, "Px", zeta, 1); in createMopacSlaters() 222 createSphericalSlaterByType(iAtom, atomicNumber, "Py", zeta, 1); in createMopacSlaters() 223 createSphericalSlaterByType(iAtom, atomicNumber, "Pz", zeta, 1); in createMopacSlaters() 226 createSphericalSlaterByType(iAtom, atomicNumber, "Dx2-y2", zeta, 1); in createMopacSlaters() 227 createSphericalSlaterByType(iAtom, atomicNumber, "Dxz", zeta, 1); in createMopacSlaters() 228 createSphericalSlaterByType(iAtom, atomicNumber, "Dz2", zeta, 1); in createMopacSlaters() 229 createSphericalSlaterByType(iAtom, atomicNumber, "Dyz", zeta, 1); in createMopacSlaters() 230 createSphericalSlaterByType(iAtom, atomicNumber, "Dxy", zeta, 1); in createMopacSlaters() 244 protected void createSphericalSlaterByType(int iAtom, int atomicNumber, in createSphericalSlaterByType() argument [all …]
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H A D | JaguarReader.java | 131 int iAtom = 0; in readCharges() local 137 asc.atoms[iAtom++].partialCharge = parseFloatStr(tokens[i]); in readCharges() 168 int iAtom = 0; in readUnnormalizedBasis() local 181 iAtom++; in readUnnormalizedBasis() 188 sdata[iFunc][0] = iAtom; in readUnnormalizedBasis() 254 int iAtom = 0; in readBasisNormalized() local 270 iAtom++; in readBasisNormalized() 296 sdata = new int[] { iAtom, iType, gaussianCount + 1, 1, iFunc }; in readBasisNormalized()
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H A D | DgridReader.java | 157 int iAtom = parseIntStr(tokens[i++]) - 1; in readMolecularOrbitals() local 159 String key = iAtom + "_" + code; in readMolecularOrbitals() 167 addSlater(createSlaterData(iAtom + 1, atoms[iAtom].elementSymbol, code), n); in readMolecularOrbitals() 227 private SlaterData createSlaterData(int iAtom, String atomSymbol, String xyz) { in createSlaterData() argument 282 return new SlaterData(iAtom, x, y, z, r, zeta, 1); in createSlaterData()
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/ |
H A D | fix_neighlist_mesh.cpp | 307 int iAtom = binhead[iBin]; in checkBin() local 310 while(iAtom != -1) in checkBin() 312 if((iAtom > nlocal) && (!domain->is_periodic_ghost(iAtom))) in checkBin() 314 if(bins) iAtom = bins[iAtom]; in checkBin() 315 else iAtom = -1; in checkBin() 322 if(bins) iAtom = bins[iAtom]; in checkBin() 323 else iAtom = -1; in checkBin() 339 neighbors.push_back(iAtom); in checkBin() 347 neighbors.push_back(iAtom); in checkBin() 351 if(bins) iAtom = bins[iAtom]; in checkBin() [all …]
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/dports/science/dftbplus/dftbplus-19.1/prog/dftb+/lib_derivs/ |
H A D | numderivs2.F90 | 38 integer :: iAtom component 101 self%iAtom = 1 105 xInit(self%iComponent,self%iAtom) = & 106 & xInit(self%iComponent,self%iAtom) + self%iDelta*self%Delta 132 if (self%iAtom==self%nDerivs .and. self%iComponent == 3 .and. & 141 self%derivs((ii-1)*3+jj,(self%iAtom-1)*3+self%iComponent) = & 142 & self%derivs((ii-1)*3+jj,(self%iAtom-1)*3+self%iComponent) & 153 if (self%iComponent == 3) self%iAtom = self%iAtom + 1 158 xNew(self%iComponent,self%iAtom) = xNew(self%iComponent,self%iAtom) + &
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/dports/science/jdftx/jdftx-1.6.0/jdftx/phonon/ |
H A D | Phonon.cpp | 402 for(int iAtom=0; iAtom<nAtoms; iAtom++) in dgradSymmetrize() local 446 for(int iAtom=0; iAtom<nAtoms; iAtom++) in forceMatrixGammaPrimeFix() local 455 V[iAtom][jAtom] += w * dr; in forceMatrixGammaPrimeFix() 463 for(int iAtom=0; iAtom<nAtoms; iAtom++) in forceMatrixGammaPrimeFix() local 466 Vr[iAtom] += wV; in forceMatrixGammaPrimeFix() 472 for(int iAtom=0; iAtom<nAtoms; iAtom++) in forceMatrixGammaPrimeFix() local 495 for(int iAtom=0; iAtom<nAtoms; iAtom++) in forceMatrixGammaPrimeFix() local 510 for(int iAtom=0; iAtom<nAtoms; iAtom++) in forceMatrixGammaPrimeFix() local 512 mask.set(iAtom*3+iDir,iDir, 1.); in forceMatrixGammaPrimeFix() 520 for(int iAtom=0; iAtom<nAtoms; iAtom++) in forceMatrixGammaPrimeFix() local [all …]
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/dports/science/iboview/ibo-view.20150427/src/IboView/ |
H A D | CtDftGrid_ivb.cpp | 122 void GetAtomGridParams( uint &nRadialPt, double &AtomicScale, uint &iAngGrid, uint iAtom ); 126 FScalar GetPairVoronoiR(double Mu, size_t iAtom, size_t iOtherAtom); 163 FScalar FDftGridGenerator::GetPairVoronoiR(double Mu, size_t iAtom, size_t iOtherAtom) in GetPairVoronoiR() argument 171 assert( Atoms[iAtom].AtomicNumber < nRadii ); in GetPairVoronoiR() 175 R1 = CovalentRadii[Atoms[iAtom].AtomicNumber - 1], in GetPairVoronoiR() 266 if (iCenterAtom == iAtom) in GetAtomWeight() 328 &Atom = Atoms.Atoms[iAtom]; in GetAtomGridParams() 407 &Atom = Atoms.Atoms[iAtom]; in AddAtomGrid() 418 GetAtomGridParams(nr, AtomicScale, iBaseAngGrid, iAtom); in AddAtomGrid() 525 for ( uint iAtom = 0; iAtom < Atoms.size(); ++ iAtom ) { in Create() local [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapesurface/ |
H A D | LcaoCartoon.java | 232 private void setLcaoOn(int iAtom, boolean TF) { in setLcaoOn() argument 233 String id = getID(lcaoID, iAtom); in setLcaoOn() 251 private void deleteLcaoCartoon(int iAtom) { in deleteLcaoCartoon() argument 252 String id = getID(lcaoID, iAtom); in deleteLcaoCartoon() 268 private void createLcaoCartoon(int iAtom) { in createLcaoCartoon() argument 269 String id = getID(lcaoID, iAtom); in createLcaoCartoon() 281 … setPropI("colorRGB", Integer.valueOf(vwr.gdata.getColorArgbOrGray(ms.at[iAtom].colixAtom)), null); in createLcaoCartoon() 291 setPropI("atomIndex", Integer.valueOf(iAtom), null); in createLcaoCartoon() 293 V3.newV(ms.at[iAtom]), new V3() }; in createLcaoCartoon() 312 || vwr.getHybridizationAndAxes(iAtom, axes[0], axes[1], thisType) != null) { in createLcaoCartoon() [all …]
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/dports/science/jdftx/jdftx-1.6.0/jdftx/wannier/ |
H A D | WannierMinimizer_phonon.cpp | 128 for(int iAtom=0; iAtom<nAtoms; iAtom++) in saveMLWF_phonon() local 129 { int iMode = 3*iAtom + iDir; in saveMLWF_phonon() 143 for(int iAtom=0; iAtom<nAtoms; iAtom++) in saveMLWF_phonon() local 144 { int iMode = 3*iAtom + iDir; in saveMLWF_phonon() 257 for(size_t iAtom=0; iAtom<xAtoms.size(); iAtom++) in saveMLWF_phonon() local 258 { matrix w1i = entry1.second(iAtom,iAtom+1, 0,xExpect.size()); in saveMLWF_phonon() 259 matrix w2i = entry2.second(iAtom,iAtom+1, 0,xExpect.size()); in saveMLWF_phonon()
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/dports/science/xtb/xtb-6.4.1/src/ |
H A D | model_hessian.f90 | 2163 ixyz(i,iAtom) = (iAtom-1)*3 + i 2401 Hess(Ind(icoor,iAtom,jcoor,iAtom))= & 2483 Hess(Ind(icoor,iAtom,jcoor,iAtom))= & 2628 Hess(Ind(icoor,iAtom,jcoor,iAtom))= & 2629 & Hess(Ind(icoor,iAtom,jcoor,iAtom)) & 2726 ixyz(i,iAtom) = (iAtom-1)*3 + i 2728 Ind(i,iAtom,j,jAtom)=Jnd(Max(ixyz(i,iAtom),ixyz(j,jAtom)),& 2942 Hess(Ind(icoor,iAtom,jcoor,iAtom))=& 3018 Hess(Ind(icoor,iAtom,jcoor,iAtom))=& 3108 Hess(Ind(icoor,iAtom,jcoor,iAtom))=& [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/molxyz/ |
H A D | MolReader.java | 229 int iAtom = Integer.MIN_VALUE; in readAtomsAndBonds() local 264 if (iAtom == Integer.MIN_VALUE && haveAtomSerials) in readAtomsAndBonds() 265 iAtom = i + 1; in readAtomsAndBonds() 268 addMolAtom(iAtom, isotope, elementSymbol, charge, x, y, z); in readAtomsAndBonds() 334 int iAtom = parseIntAt(line, 3); in readAtomValues() local 335 if (iAtom < 1 || iAtom > atomCount) { in readAtomValues() 336 Logger.error("V nnn does not evalute to a valid atom number: " + iAtom); in readAtomValues() 340 atomData[iAtom - 1] = s; in readAtomValues() 431 public void addMolAtom(int iAtom, int isotope, String elementSymbol, in addMolAtom() argument 454 if (iAtom == Integer.MIN_VALUE) { in addMolAtom() [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/api/ |
H A D | PymolAtomReader.java | 5 int getUniqueID(int iAtom); in getUniqueID() argument 7 float getVDW(int iAtom); in getVDW() argument 9 int getCartoonType(int iAtom); in getCartoonType() argument
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/symmetry/ |
H A D | CIPData.java | 273 private int checkEne(BS bsAllEnes, BS bsPath, int iLast, int iAtom, int order, BS bsEneAtom1) { in checkEne() argument 274 if (bsPath.get(iAtom)) in checkEne() 275 return (bsEneAtom1.get(iAtom) == (order == 2) ? iAtom : -1); in checkEne() 276 bsPath.set(iAtom); in checkEne() 277 SimpleNode a = atoms[iAtom]; in checkEne() 281 bsEneAtom1.set(iAtom); in checkEne() 288 && (isLoop = checkEne(bsAllEnes, bsPath, iAtom, iNext, 3 - order, bsEneAtom1)) >= 0) { in checkEne() 292 bsKekuleAmbiguous.set(iAtom); in checkEne() 293 bsEnes.clear(iAtom); in checkEne() 295 return isLoop == iAtom ? -1 : isLoop; in checkEne()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/jvxl/readers/ |
H A D | IsoIntersectAtomReader.java | 183 for (int iAtom = bs.nextSetBit(0); iAtom >= 0; iAtom = bs.nextSetBit(iAtom + 1)) { in getValueAtPoint2() 184 float r = pt.distance(atomXyzTruncated[iAtom]) - atomRadius[iAtom]; in getValueAtPoint2()
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H A D | IsoIntersectReader.java | 183 for (int iAtom = bs.nextSetBit(0); iAtom >= 0; iAtom = bs.nextSetBit(iAtom + 1)) { in getValueAtPoint2() 184 float r = pt.distance(atomXyzTruncated[iAtom]) - atomRadius[iAtom]; in getValueAtPoint2()
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H A D | AtomDataReader.java | 483 for (int iAtom = myAtomCount; --iAtom >= 0;) { in getAtomMinMax() 484 if (bs != null && !bs.get(iAtom)) in getAtomMinMax() 486 setGridLimitsForAtom(atomXyzTruncated[iAtom], atomRadius[iAtom], pt0, pt1); in getAtomMinMax() 488 bsAtomMinMax[i].set(iAtom); in getAtomMinMax() 504 for (int iAtom = thisAtomSet.nextSetBit(0); iAtom >= 0; iAtom = thisAtomSet in markSphereVoxels() 505 .nextSetBit(iAtom + 1)) { in markSphereVoxels() 506 if (!havePlane && validSpheres != null && !validSpheres.get(iAtom)) in markSphereVoxels() 509 boolean isNearby = (iAtom >= firstNearbyAtom); in markSphereVoxels() 510 P3 ptA = atomXyzTruncated[iAtom]; in markSphereVoxels() 511 float rA = atomRadius[iAtom]; in markSphereVoxels() [all …]
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/dports/science/ergo/ergo-3.8/source/ |
H A D | fermi_contact.cc | 165 for(int iAtom=0; iAtom<molecule.getNoOfAtoms(); iAtom++) { in main() local 166 const Atom &atom = molecule.getAtom(iAtom); in main() 171 iAtom+1); in main()
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