[SIESTA-L]
Dear siesta users can you help me? i did the run for fdf file, and i found this error.. coor: Atomic-coordinates input format = Cartesian coordinates coor: (in Angstroms) rcut: Wrong species 3. Have 1 Stopping Program from Node:0 Program aborted. Backtrace: siesta: Atomic coordinates (Bohr) and species siesta: 5.66918** 5.66918 31 siesta: 5.66918** 5.66918 32 siesta: 5.66918** 7.55891 33 siesta: 5.66918** 7.55891 34 siesta: 3.77945** 9.44863 25 siesta: 3.77945** 9.44863 26 siesta: 1.88973** 9.44863 17 siesta: 1.88973** 9.44863 18 siesta: 0.0** 7.55891 09 siesta: 0.0** 7.55891 0 10 siesta: -0.0** 5.66918 0 11 siesta: -0.0** 5.66918 0 12 siesta: 0.0** 3.77945 0 13 siesta: 0.0** 3.77945 0 14 siesta: 1.88973** 1.88973 1 15 siesta: 1.88973** 1.88973 1 16 siesta: 3.77945** 1.88973 2 17 siesta: 3.77945** 1.88973 2 18 siesta: 5.66918** 3.77945 3 19 siesta: 5.66918** 3.77945 3 20 siesta: Automatic unit cell vectors (Ang): siesta:5.8135000.000.00 siesta:0.000.00 siesta:0.000.00 10.213500 rcut: Wrong species 3. Have 1 Stopping Program from Node:0 #0 0x7f1e771a8d21 in ??? #1 0x7f1e771a97ad in ??? #2 0x7f1e773fd38c in ??? #3 0x562eeed87aca in ??? #4 0x562eeeac6e83 in ??? #5 0x562eeea4cd25 in ??? #6 0x562eeea79d0b in ??? #7 0x562eeea78277 in ??? #8 0x562eee9bd74c in ??? #9 0x7f1e76e24082 in __libc_start_main at ../csu/libc-start.c:308 #10 0x562eee9bd81d in ??? #11 0x in ??? and this is the fdf file.. # Created by GDIS version 0,90.0 # SystemLabel nano55 NumberOfAtoms20 NumberOfSpecies 1 %block ChemicalSpeciesLabel 16 C %endblock ChemicalSpeciesLabel LatticeConstant 1.0 Ang %block LatticeVectors 7,3128000,000,00 -3,6564006,33307057280,00 0,000,004,280600 %endblock LatticeVectors AtomicCoordinatesFormat NotScaledCartesianAng %block AtomicCoordinatesAndAtomicSpecies 3,811431360 3,166535286 1,4211592001 3,811431360 3,166535286 0,01 3,432628320 4,331820272 3,5614592001 3,432628320 4,331820272 2,140301 2,441012640 5,052523703 1,4211592001 2,441012640 5,052523703 0,01 1,215387360 5,052523703 3,5614592001 1,215387360 5,052523703 2,140301 0,224502960 4,331820272 1,4211592001 0,224502960 4,331820272 0,01 -0,155031360 3,166535286 3,5614592001 -0,155031360 3,166535286 2,140301 0,223771680 2,001250301 1,4211592001 0,223771680 2,001250301 0,01 1,215387360 1,280546870 3,5614592001 1,215387360 1,280546870 2,140301 2,441012640 1,280546870 1,4211592001 2,441012640 1,280546870 0,01 3,431897040 2,001250301 3,5614592001 3,431897040 2,001250301 2,140301 %endblock AtomicCoordinatesAndAtomicSpecies PAO.BasisTypesplit PAO.BasisSizeDZP SolutionMethod diagon Harris_functionalfalse XC.functionalLDA XC.AuthorsPZ SpinPolarizedfalse MeshCutoff100,00 Ry kgrid_cutoff0,00 Bohr ElectronicTemperature300,00 K MaxSCFIterations50 DM.NumberPulay0 DM.MixingWeight0,25 MD.TypeOfRunCG MD.VariableCellfalse MD.MaxCGDispl0,20 Bohr MD.PreconditionVariableCell5,00 Ang MD.MaxStressTol1,00 GPa %block MD.TargetStress -1,00 -1,00 -1,00 0,00 0,00 0,00 %endblock MD.TargetStress MD.MaxForceTol0,04 eV/Ang MD.InitialTimeStep1 MD.FinalTimeStep1 MD.LengthTimeStep1 fs MD.InitialTemperature0,00 K MD.Quenchfalse MD.TargetTemperature0,00 K MD.NoseMass100,00 Ry*fs**2 MD.ParrinelloRahmanMass100,00 Ry*fs**2 MD.AnnealOptionTemperatureandPressure MD.TauRelax100,00 fs MD.BulkModulus100,00 Ry/Bohr**3 MD.TargetPressure0,00 GPa MD.FCDispl0,04 Bohr MD.FCfirst1 MD.FClast0 UseSaveData false WriteCoorInitaltrue WriteCoorStepfalse WriteForces false WriteKpoints false WriteEigenvalues false WriteKbands false WriteBands false WriteWaveFunctions false WriteMullikenPop 0 WriteDM true WriteCoorXmol false WriteCoorCerius false WriteMDXmol
[SIESTA-L]
Users Siesta I want run denchar. I wrote the Flags dépend of it but *.wFSX not found. What is the Problem, if *.WFSX not existe after run fdf file? -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L]
Dear Siesta Users I make run to carbone nanotube armchair, but i find an error, can anyone helle me to solve this error? ( I added also fdf file here) FDF module: fdf_bline: block_fdf structure not initialized File: fdf.F90 Line: 2803 * STOP Stopping Program FDF file: SystemLabel arm NumberOfAtoms12 NumberOfSpecies 1 %block ChemicalSpeciesLabel 16 C %endblock ChemicalSpeciesLabel LatticeConstant 1.0 Ang %block LatticeVectors 25.000 0.0 0.0 0.000 2.501081300.0 0. 25.0 0.0 #%endblock LatticeVectors #%block LatticeParameters # 7,476200 7,476200 2,464300 90,00 90,00 120,00 #%endblock LatticeParameters AtomicCoordinatesFormat Ang %block AtomicCoordinatesAndAtomicSpecies 0,77620 0,5 0,01 0,81380 0,70610 0,01 0,77620 0,77620 0,51 0,60770 0,81380 0,51 0,5 0,77620 0,01 0,29390 0,60770 0,01 0,22380 0,5 0,51 0,18620 0,29390 0,51 0,22380 0,22380 0,01 0,39230 0,18620 0,01 0,5 0,22380 0,51 0,70610 0,39230 0,51 %endblock AtomicCoordinatesAndAtomicSpecies PAO.BasisTypesplit PAO.BasisSizeDZP PAO.EnergyShift 50 meV SolutionMethod diagon PAO.SplitNorm0,15 XC.functionalLDA XC.AuthorsPZ SpinPolarizedfalse MeshCutoff300,00 Ry %block kgrid_Monkhorst_Pack 10 0 0 0.0 0 1 0 0.0 0 0 10 0.0 %endblock kgrid_Monkhorst_Pack MD.MaxForceTol0,005 eV/Ang MD.InitialTimeStep1 MD.FinalTimeStep 1 MD.LengthTimeStep1 fs MD.NumCGsteps 0 MD.TypeOfRun CG DM.MixingWeight 0.02 WriteCoorXmoltrue WriteMDXmol true WriteMullikenPop 1 DM.NumberPulay 5 ElectronicTemperature300,00 K MaxSCFIterations500 DM.Tolerance 1.d-5 SolutionMethod diagon TS.WriteHS true DM.UseSaveDM true UseSaveData true MD.UseSaveXV true MD.UseSaveCG true %block BandLines 10.0 0.0 0.0 \Gamma 50 0.0 0.0 0.5 X 100 0.0 0.0 0.0 \Gamma %endblock BandLines %block ProjectedDensityOfStates -30.00 20.00 0.2 1000 eV %endblock ProjectedDensityOfStates %block PAO.basis C3 .35201 n=2 0 2 E50.37145 5.22551 5.43077 3.08484 1.0 1.0 n=2 1 2 E13.53326 6.81234 6.83094 3.01366 1.0 1.0 n=2 2 1 E 110.78225 .01065 5.04748 1.0 %endblock PAO.basis -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L]
Siesta Users I want to find Band structure and DOS for carbone nanotube (in his 2 types). So i have to fdf file, and to know how specify the details of fdf file in 2 types. Know you any Website or tutorials for this project?! Regards -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L]
Siesta Users I want to find Band structure and DOS for carbone nanotube (in his 2 types). So i have to fdf file, and to know how specify the details of fdf file in 2 types. Know you any Website or tutorials for this project?! Regards -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L]
Hello When i run pdos.dat for different orbital after change the "m.orbital_chouser.f90" the output is: STOP data array full *How solve this Problem?!* *Please help* -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L]
Hello When i plot the Band of graphene, the Band gap it's not Zero. So what ist the Part of FdF depend of the Band gap? -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L]
Hello How can resolve "xv File not round" in running ? While i have : UseSaveData T DM.UseSaveDM T -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L]
Hello When i run the simulation of Carbone , i existe this error . Any Idea about this error , and how can resolve it ?! Please Help.. Best regard siesta: WARNING: XV file not found siesta: Atomic coordinates (Bohr) and species siesta: 0.0** 3.77945 01 siesta: Automatic unit cell vectors (Ang): siesta:0.000.000.00 siesta:0.000.000.00 siesta:0.000.000.00 rcut: Wrong species 0. Have 1 Stopping Program from Node:0 #0 0x7f0bf0cdbd21 in ??? #1 0x7f0bf0cdc7ad in ??? #2 0x7f0bf0f3038c in ??? #3 0x55c259359aca in ??? #4 0x55c259098e83 in ??? #5 0x55c25901ed25 in ??? #6 0x55c25904bd0b in ??? #7 0x55c25904a277 in ??? #8 0x55c258f8f74c in ??? #9 0x7f0bf0957082 in __libc_start_main at ../csu/libc-start.c:308 #10 0x55c258f8f81d in ??? #11 0x in ??? -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] [***Posible SPAM***] Re:
Hi How can make an Access to the executable File, typically located in the Filder./obj ? Best regard. Amal Yassin schrieb am So., 31. Juli 2022, 18:07: > Hello all, > > I have downloaded an Atom program, but some Atoms are not in it, How do I get > their PSf file?! > > > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] [***Posible SPAM***]
Hello all, I have downloaded an Atom program, but some Atoms are not in it, How do I get their PSf file?! -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L]
Hello all How to run DENCHAR ?! Amal Yassin schrieb am Fr., 24. Juni 2022, 22:18: > Hello > How to create ans Check an arch.make file?! > > > RCP schrieb am Fr., 24. Juni 2022, 22:07: > >> Hi, those are routines from the BLAS library, seems you're missing it. >> Check your arch.make file. >> Bye, >> Roberto >> >> On 22/06/2022 18:14, Ghazanfari, Sarah wrote: >> > Hello all, >> > >> > I am trying to compile siesta in parallel version; however, I face the >> following >> > errors. I greatly appreciate it if someone can help me. >> > >> > denmat.o: In function `m_denmat_mp_denmat_': >> > denmat.F:(.text+0x1f01): undefined reference to `dscal_' >> > denmat.F:(.text+0x1f22): undefined reference to `dscal_' >> > dhscf.o: In function `m_dhscf_mp_dhscf_': >> > dhscf.F:(.text+0x4891): undefined reference to `ddot_' >> > dhscf.F:(.text+0x48c3): undefined reference to `ddot_' >> > dhscf.F:(.text+0x4953): undefined reference to `ddot_' >> > >> > >> > >> >> -- >> SIESTA is supported by the Spanish Research Agency (AEI) and by the >> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >> > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
Re: [SIESTA-L] Siesta parallel version installation on HPC
Hello How to create ans Check an arch.make file?! RCP schrieb am Fr., 24. Juni 2022, 22:07: > Hi, those are routines from the BLAS library, seems you're missing it. > Check your arch.make file. > Bye, > Roberto > > On 22/06/2022 18:14, Ghazanfari, Sarah wrote: > > Hello all, > > > > I am trying to compile siesta in parallel version; however, I face the > following > > errors. I greatly appreciate it if someone can help me. > > > > denmat.o: In function `m_denmat_mp_denmat_': > > denmat.F:(.text+0x1f01): undefined reference to `dscal_' > > denmat.F:(.text+0x1f22): undefined reference to `dscal_' > > dhscf.o: In function `m_dhscf_mp_dhscf_': > > dhscf.F:(.text+0x4891): undefined reference to `ddot_' > > dhscf.F:(.text+0x48c3): undefined reference to `ddot_' > > dhscf.F:(.text+0x4953): undefined reference to `ddot_' > > > > > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank
Hello How to solve the Error of (arch.make) during the compilation of Siesta ?! Please Help !! -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
