Commit 4392a5e6 authored by Ask Hjorth Larsen's avatar Ask Hjorth Larsen

add smeagol test cases

parent 52786f60
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#!/bin/sh
#SBATCH -n 32
#SBATCH -t 30:00
#SBATCH -p debug
##SBATCH -U physics
##SBATCH --mem=100
mpirun -n 32 /projects/pi-ssanvito/parsons/drogheta/smeagol_acmol_soc_kshift_bond_currents/Smeagol/Src/smeagol-1.2_acmol/Src/smeagol-1.2_csg < input.fdf > Au.out
6
Au 0.853483 1.478277 0.000000
Au 3.413937 0.000000 0.000000
Au 0.000000 0.000000 2.414000
Au 2.560449 1.478277 2.414000
Au 1.706973 0.000000 4.828000
Au 4.267422 1.478277 4.828000
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6
1 -0.000024 -0.003333 -0.000012
2 0.003750 -0.000030 -0.000017
3 -0.011705 -0.000036 -0.241348
4 -0.011589 0.000441 -0.241619
5 0.011402 -0.000036 0.241855
6 0.011517 0.000447 0.241605
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176
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2 0.000000 -0.281144 0.000000 0.00312500000000
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4 0.324642 -0.281144 0.000000 0.00312500000000
5 -0.162321 0.000000 0.000000 0.00312500000000
6 0.000000 0.000000 0.000000 0.00312500000000
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10 0.000000 0.281144 0.000000 0.00312500000000
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107 0.162321 0.281144 0.137735 0.00625000000000
108 0.324642 0.281144 0.137735 0.00625000000000
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176 0.324642 0.562287 0.229558 0.00312500000000
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9.677102368 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
0.000000000 5.587166487 0.000000000 0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 13.685402049 0.000000000 0.000000000 0.000000000
6
1 79 1.612849765 2.793539780 0.000000000 0.000000000 0.000000000 0.000000000
1 79 6.451408508 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
1 79 0.000000000 0.000000000 4.561800683 0.000000000 0.000000000 0.000000000
1 79 4.838549294 2.793539780 4.561800683 0.000000000 0.000000000 0.000000000
1 79 3.225712758 0.000000000 9.123601366 0.000000000 0.000000000 0.000000000
1 79 8.064262052 2.793539780 9.123601366 0.000000000 0.000000000 0.000000000
Allocation summary at 2016/07/12 18:29:41.470 +01:00
Present memory allocation: 0.000000 Mbyte
Maximum memory allocation: 0.000000 Mbyte
Occurred after allocating:
In routine:
Present memory all nodes : 0.000000 Mbyte
6
Au 0.853483 1.478277 0.000000
Au 3.413937 0.000000 0.000000
Au 0.000000 0.000000 2.414000
Au 2.560449 1.478277 2.414000
Au 1.706973 0.000000 4.828000
Au 4.267422 1.478277 4.828000
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#
SystemName Au_device # optional change
SystemLabel AuLead
#********************************************************
# Specification of atomic species and positions
#********************************************************
# Chemical species
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 79 Au
%endblock ChemicalSpeciesLabel
# UNIT CELL
LatticeConstant 1.0 Ang
%block LatticeVectors
5.1209 0.0000000000 0.0000000000
0.0000000000 2.9566 0.0000000000
0.0000000000 0.0000000000 7.242
%endblock LatticeVectors
# ATOMIC POSITIONS
NumberOfAtoms 6
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.853483000 1.478277000 0.000000000 1
3.413937000 0.000000000 0.000000000 1
0.000000000 -0.000000000 2.414000000 1
2.560449000 1.478277000 2.414000000 1
1.706973000 0.000000000 4.828000000 1
4.267422000 1.478277000 4.828000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
#********************************************************
# DFT options
#********************************************************
# Basis set variables
PAO.BasisType split
PAO.EnergyShift 0.02700000000 eV
%block PAO.Basis
Au 3 # Species label, number of l-shells
n=6 0 2 # n, l, Nzeta, Polarization, NzetaPol
6.0 0.0
n=6 1 2 # n, l, Nzeta, Polarization, NzetaPol
5.0 0.0
n=5 2 2 # n, l, Nzeta
4.0 0.0
%endblock PAO.Basis
%block kgrid_Monkhorst_Pack
4 0 0 0.0
0 4 0 0.0
0 0 20 0.0
%endblock kgrid_Monkhorst_Pack
# General variables
ElectronicTemperature 200 K
MeshCutoff 300. Ry
xc.functional LDA # Exchange-correlation functional
xc.authors CA
#SpinPolarized T
#SpinOrbit T
# SCF variables
DM.MixSCF1 F # optional change
MaxSCFIterations 1000 # Maximum number of SCF iter
DM.MixingWeight 0.1 # optional change
DM.Tolerance 1.0E-5
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 5
SolutionMethod diagon
#FixSpin T
#TotalSpin 0.5
# Output variables
WriteMullikenPop 0
WriteBands F
SaveRho T
SaveElectrostaticPotential T
SaveTotalPotential F
WriteCoorXmol T
WriteMDXmol T
#********************************************************
# SMEAGOL options
#********************************************************
#ParallelOverK T
BulkTransport T
BulkLead LR
WriteEDM T
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el: Routine,Calls,Time Elapsed,% = IterSCF 1 735.818 96.14
el: ELAPSED times:
el: Routine Calls Time/call Tot.time %
elap: siesta 1 7304.264 7304.264 100.00
elap: Setup 1 18.292 18.292 0.25
elap: bands 1 0.047 0.047 0.00
elap: writewave 1 0.102 0.102 0.00
elap: KSV_init 1 0.046 0.046 0.00
elap: IterMD 1 7026.863 7026.863 96.20
elap: hsparse 2 1.031 2.062 0.03
elap: overfsm 2 2.367 4.734 0.06
elap: IterSCF 13 539.571 7014.428 96.03
elap: kinefsm 2 1.837 3.675 0.05
elap: nlefsm 2 31.506 63.011 0.86
elap: DHSCF 14 10.808 151.315 2.07
elap: DHSCF1 1 2.542 2.542 0.03
elap: DHSCF2 1 43.644 43.644 0.60
elap: REORD 146 0.000 0.051 0.00
elap: POISON 15 0.107 1.601 0.02
elap: DHSCF3 14 7.107 99.494 1.36
elap: rhoofd 14 1.282 17.955 0.25
elap: CELLXC 14 0.084 1.179 0.02
elap: vmat 13 5.588 72.650 0.99
elap: diagon 12 562.944 6755.326 92.48
elap: cdiag 4224 1.554 6563.716 89.86
elap: DHSCF4 1 5.155 5.155 0.07
elap: dfscf 1 2.233 2.233 0.03
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dHmax dDmax Ef(eV)
1 -6857.1459 -6803.5679 -6803.5679 0.49498 0.00000 0.84586
2 -6867.8297 -6813.8203 -6813.8317 0.85403 0.00000 -3.11485
3 -6838.4859 -6820.0726 -6820.0739 0.36568 0.00000 -1.71778
4 -6838.3691 -6821.6901 -6821.6920 0.30487 0.00000 -1.60540
5 -6838.3609 -6837.9361 -6837.9386 0.00691 0.00000 -1.60377
6 -6838.3607 -6838.0561 -6838.0586 0.00604 0.00000 -1.59977
7 -6838.3607 -6838.3078 -6838.3103 0.00042 0.00000 -1.59986
8 -6838.3607 -6838.3194 -6838.3219 0.00034 0.00000 -1.59953
9 -6838.3606 -6838.3608 -6838.3633 0.00003 0.00000 -1.59963
10 -6838.3606 -6838.3609 -6838.3634 0.00002 0.00000 -1.59963
11 -6838.3606 -6838.3609 -6838.3634 0.00001 0.00000 -1.59963
12 -6838.3606 -6838.3607 -6838.3632 0.00000 0.00000 -1.59963
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#
SystemName Au_device # optional change
SystemLabel AuLead
#********************************************************
# Specification of atomic species and positions
#********************************************************
# Chemical species
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 79 Au
%endblock ChemicalSpeciesLabel
# UNIT CELL
LatticeConstant 1.0 Ang
%block LatticeVectors
5.1209 0.0000000000 0.0000000000
0.0000000000 2.9566 0.0000000000
0.0000000000 0.0000000000 7.242
%endblock LatticeVectors
# ATOMIC POSITIONS
NumberOfAtoms 6
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.853483000 1.478277000 0.000000000 1
3.413937000 0.000000000 0.000000000 1
0.000000000 -0.000000000 2.414000000 1
2.560449000 1.478277000 2.414000000 1
1.706973000 0.000000000 4.828000000 1
4.267422000 1.478277000 4.828000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
#********************************************************
# DFT options
#********************************************************
# Basis set variables
PAO.BasisType split
PAO.EnergyShift 0.02700000000 eV
%block PAO.Basis
Au 3 # Species label, number of l-shells
n=6 0 2 # n, l, Nzeta, Polarization, NzetaPol
6.0 0.0
n=6 1 2 # n, l, Nzeta, Polarization, NzetaPol
5.0 0.0
n=5 2 2 # n, l, Nzeta
4.0 0.0
%endblock PAO.Basis
%block kgrid_Monkhorst_Pack
4 0 0 0.0
0 4 0 0.0
0 0 20 0.0
%endblock kgrid_Monkhorst_Pack
# General variables
ElectronicTemperature 200 K
MeshCutoff 300. Ry
xc.functional LDA # Exchange-correlation functional
xc.authors CA
#SpinPolarized T
#SpinOrbit T
# SCF variables
DM.MixSCF1 F # optional change
MaxSCFIterations 1000 # Maximum number of SCF iter
DM.MixingWeight 0.1 # optional change
DM.Tolerance 1.0E-5
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 5
SolutionMethod diagon
#FixSpin T
#TotalSpin 0.5
# Output variables
WriteMullikenPop 0
WriteBands F
SaveRho T
SaveElectrostaticPotential T
SaveTotalPotential F
WriteCoorXmol T
WriteMDXmol T
#********************************************************
# SMEAGOL options
#********************************************************
#ParallelOverK T
BulkTransport T
BulkLead LR
WriteEDM T
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###############################################################################
TCHPC Cluster: parsons
Job 63878 (Au.sh) for User 'drogheta' in Account 'physics'
Finished at: Tue Jul 12 18:29:42 IST 2016
Job completion status:
======================
JobID JobName AllocCPUS NTasks NNodes MaxRSS MaxRSSNode MaxDiskRead MaxDiskWrite Elapsed State ExitCode
------------ ---------- --------- ------ ------ ---------- ------------- ------------ ------------ ---------- ---------- --------
63878 Au.sh 32 4 00:03:52 COMPLETED 0:0
63878.batch batch 8 1 1 472376K parsons-n001 0.01M 0.00M 00:03:52 COMPLETED 0:0
63878.0 orted 3 3 3 00:03:51 COMPLETED 0:0
Job details:
============
JobId=63878 JobName=Au.sh
UserId=drogheta(1350) GroupId=drogheta(1503)
Priority=348858 Nice=0 Account=physics QOS=normal
JobState=COMPLETING Reason=None Dependency=(null)
Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
DerivedExitCode=0:0
RunTime=00:03:52 TimeLimit=00:30:00 TimeMin=N/A
SubmitTime=2016-07-12T16:27:28 EligibleTime=2016-07-12T16:27:28
StartTime=2016-07-12T18:25:50 EndTime=2016-07-12T18:29:42
PreemptTime=None SuspendTime=None SecsPreSuspend=0
Partition=debug AllocNode:Sid=parsons01:17796
ReqNodeList=(null) ExcNodeList=(null)
NodeList=parsons-n004
BatchHost=parsons-n001
NumNodes=1 NumCPUs=8 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
TRES=cpu=32,mem=60000,node=4