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/dports/science/nwchem-data/nwchem-7.0.2-release/src/dplot/
H A Dget_charges.F30 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 …]
H A Dget_grid.F24 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
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/dplot/
H A Dget_charges.F30 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 …]
H A Dget_grid.F24 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
/dports/science/nwchem-data/nwchem-7.0.2-release/src/dimqm/
H A Ddimqm_f2d.F30 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 …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/dimqm/
H A Ddimqm_f2d.F30 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 …]
/dports/science/dftbplus/dftbplus-19.1/prog/dftb+/lib_dftb/
H A Dsccinit.F90308 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 …]
H A Dspin.F9068 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)
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/quantum/
H A DMopacSlaterReader.java218 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 …]
H A DJaguarReader.java131 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()
H A DDgridReader.java157 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()
/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/
H A Dfix_neighlist_mesh.cpp307 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 …]
/dports/science/dftbplus/dftbplus-19.1/prog/dftb+/lib_derivs/
H A Dnumderivs2.F9038 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) + &
/dports/science/jdftx/jdftx-1.6.0/jdftx/phonon/
H A DPhonon.cpp402 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 …]
/dports/science/iboview/ibo-view.20150427/src/IboView/
H A DCtDftGrid_ivb.cpp122 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 …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapesurface/
H A DLcaoCartoon.java232 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 …]
/dports/science/jdftx/jdftx-1.6.0/jdftx/wannier/
H A DWannierMinimizer_phonon.cpp128 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()
/dports/science/xtb/xtb-6.4.1/src/
H A Dmodel_hessian.f902163 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 …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/molxyz/
H A DMolReader.java229 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 …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/api/
H A DPymolAtomReader.java5 int getUniqueID(int iAtom); in getUniqueID() argument
7 float getVDW(int iAtom); in getVDW() argument
9 int getCartoonType(int iAtom); in getCartoonType() argument
/dports/science/jmol/jmol-14.32.7/src/org/jmol/symmetry/
H A DCIPData.java273 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()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/jvxl/readers/
H A DIsoIntersectAtomReader.java183 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()
H A DIsoIntersectReader.java183 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()
H A DAtomDataReader.java483 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 …]
/dports/science/ergo/ergo-3.8/source/
H A Dfermi_contact.cc165 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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