Hey Mina, I got a similar issue. They could be different ways to solve it but the way my case was solved was the following: To solve that you have to use chemistry software marvin sketch or any similar to draw the molecule you. You might find atoms very very close. Another way would be changing the unit cell which seems too large. I could be wrong for the second suggestion but that worked for me when i changed it. Looking forward to how that works out for you. EL-Abed
El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group | School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 ________________________________ From: siesta-l-requ...@uam.es <siesta-l-requ...@uam.es> on behalf of Mina Sedighi <msedi...@uwaterloo.ca> Sent: Wednesday, 20 February 2019 11:30 AM To: siesta-l Subject: Re: [SIESTA-L] Error in Cholesky factorisation in cdiag Dear Nick and Sullah, Thank you for your reply. My .fdf file commands are as follow: SystemLabel batt_str SystemName battery NumberOfSpecies 7 NumberOfAtoms 4785 %block ChemicalSpeciesLabel 1 7 N 2 6 C 3 8 O 4 1 H 5 16 S 6 30 Zn 7 25 Mn %endblock ChemicalSpeciesLabel PAO.BasisType split PAO.BasisSize DZP PAO.EnergyShift 0.01 RY MeshCutoff 500 Ry kgrid.Cutoff 8.73 Ang # half of the smallest lattice vector SCF.Mix Hamiltonian SCF.Mixer.Method Pulay MaxSCFIterations 10000 SCF.H.Tolerance 1.d-3 ev SCF.Mixer.Weight 0.3 ElectronicTemperature 300 K MD.TypeOfRun CG MD.Steps 500 MD.MaxDispl 0.05 Ang MD.MaxForceTol 0.04 ev/Ang atom from 4653 to 4785 LatticeConstant 1 Ang %block LatticeVectors 17.4600000000 0.0000000000 0.0000000000 -20.0000000000 34.6410161514 0.0000000000 0.0000000000 0.0000000000 116.9600000000 %endblock LatticeVectors SystemLabel.STRUCT_OUT true SystemLabel.STRUCT_NEXT_ITER true LongOutput true WriteKpoints WriteKbands WriteCoorStep WriteForces WriteEigenvalues WriteWaveFunctions WriteMullikenPop 1 WriteOrbMom COOP.Write SaveElectrostaticPotential SaveTotalPotential AtomicCoordinatesFormat Ang %block AtomicCoordinatesAndAtomicSpecies … … … %endblock AtomicCoordinatesAndAtomicSpecies I perform this simulation on SHARCNET (Compute Canada) graham cluster with Siesta version 4.1-b3. Besides encountering the error that I mentioned in my last email, I receive the following warning for some atoms: siesta: WARNING: Atoms "A" "B" too close: rij = 0.000000 Ang Thank you for your advice. Best regards, Mina ________________________________ From: siesta-l-requ...@uam.es <siesta-l-requ...@uam.es> on behalf of Nick Papior <nickpap...@gmail.com> Sent: February 19, 2019 7:38:52 AM To: siesta-l Subject: Re: [SIESTA-L] Error in Cholesky factorisation in cdiag This may happen due to two atoms getting too close. Could you check your atomic coordinates at the given MD step? Den man. 18. feb. 2019 kl. 22.12 skrev Mina Sedighi <msedi...@uwaterloo.ca<mailto:msedi...@uwaterloo.ca>>: Dear Siesta users, I perform a parallel relaxation simulation with siesta version 4.1-b3 on cluster. I face the following error during simulation: Error in Cholesky factorisation in cdiag Error in Cholesky factorisation in cdiag Stopping Program from Node: 105 Stopping Program from Node: 105 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 105 in communicator MPI COMMUNICATOR 3 CREATE FROM 0 with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. Any help will be appreciated. Best regards, Mina -- Kind regards Nick
