Commit c39af793 authored by Ask Hjorth Larsen's avatar Ask Hjorth Larsen
Browse files

add several test cases. Examples provided by Andrea Droghetti

parent 0a1cd99c
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2.039100000 0.000000000 2.039100000
2.039100000 2.039100000 0.000000000
0.000000000 2.039100000 2.039100000
1
1 13 0.000000000 0.000000000 0.000000000
3.853342076 0.000000000 3.853342076 0.000000000 0.000000000 0.000000000
3.853342076 3.853342076 0.000000000 0.000000000 0.000000000 0.000000000
0.000000000 3.853342076 3.853342076 0.000000000 0.000000000 0.000000000
1
1 13 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
Allocation summary at 2016/07/07 08:35:04.401 +02:00
Present memory all nodes : 0.000000 MB
Added peak mem all nodes : 0.000000 MB
Min peak memory in a node: 0.000000 MB
Max peak memory in a node: 0.000000 MB
Maximum peak of memory occurred in node: 0
Present memory allocation: 0.000000 MB
Maximum memory allocation: 0.000000 MB
Occurred after allocating:
In routine:
Allocation summary at 2016/07/07 08:35:04.402 +02:00
Present memory all nodes : 0.000000 MB
Added peak mem all nodes : 0.000000 MB
Min peak memory in a node: 0.000000 MB
Max peak memory in a node: 0.000000 MB
Maximum peak of memory occurred in node: 1
Present memory allocation: 0.000000 MB
Maximum memory allocation: 0.000000 MB
Occurred after allocating:
In routine:
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#!/bin/bash
#SBATCH --nodes=1
#SBATCH --time=30:00
#SBATCH --ntasks=2
#SBATCH -p debug
#SBATCH --output=out.log
#SBATCH --error=err.out.log
#SBATCH --exclusive
#load the environment
ulimit -s unlimited
export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
export I_MPI_FABRICS=shm:dapl
module load intel/2016a
srun --resv-ports -N 1 -n 2 /home/andrea/siesta-4.0/Obj/siesta < input.fdf > out
\ No newline at end of file
timer: Number of nodes = 2
timer: Busiest calculating node was node = 1
timer: Times refer to node = 1
timer: Total elapsed wall-clock time (sec) = 4.840
timer: CPU times (sec):
Calc: Sum, Avge, myNode, Avg/Max = 9.627 4.813 4.839 0.995
No communications time available. Compile with -DMPI_TIMING
Tot: Sum, Avge, myNode, Avg/Max = 9.627 4.813 4.839 0.995
Program times printed if > 0.000E+00 of total
Program Calls Prg.com Prg.com Prg.tot Prg.tot Nod.avg
/Tot.com /Tot.tot/Nod.max
siesta 1 0.000 0.0000 4.839 1.0000 0.995
Setup 1 0.000 0.0000 0.421 0.0870 0.982
IterGeom 1 0.000 0.0000 4.079 0.8430 0.994
state_init 1 0.000 0.0000 0.190 0.0393 0.882
hsparse 1 0.000 0.0000 0.006 0.0012 0.875
overlap 1 0.000 0.0000 0.123 0.0254 0.780
Setup_H0 1 0.000 0.0000 1.777 0.3671 1.000
naefs 2 0.000 0.0000 0.002 0.0004 0.500
kinefsm 2 0.000 0.0000 0.117 0.0242 0.774
nlefsm 2 0.000 0.0000 1.018 0.2103 0.920
DHSCF_Init 1 0.000 0.0000 0.928 0.1917 0.977
DHSCF1 1 0.000 0.0000 0.110 0.0227 0.991
INITMESH 3 0.000 0.0000 0.049 0.0101 0.500
DHSCF2 1 0.000 0.0000 0.818 0.1690 0.973
REMESH 1 0.000 0.0000 0.213 0.0440 0.897
SPLOAD 2 0.000 0.0000 0.049 0.0101 0.500
PHION 1 0.000 0.0000 0.487 0.1006 0.979
COMM_BSC 8 0.000 0.0000 0.007 0.0014 0.549
POISON 4 0.000 0.0000 0.012 0.0025 0.917
fft 8 0.000 0.0000 0.012 0.0025 0.875
IterSCF 1 0.000 0.0000 0.827 0.1709 1.000
setup_H 1 0.000 0.0000 0.389 0.0804 0.999
DHSCF 3 0.000 0.0000 1.609 0.3324 0.963
DHSCF3 3 0.000 0.0000 1.109 0.2291 0.970
rhoofd 3 0.000 0.0000 0.705 0.1457 0.905
cellXC 3 0.000 0.0000 0.017 0.0035 0.912
vmat 2 0.000 0.0000 0.328 0.0678 0.997
compute_dm 1 0.000 0.0000 0.438 0.0905 0.995
diagon 1 0.000 0.0000 0.293 0.0605 0.992
c-eigval 132 0.000 0.0000 0.131 0.0271 0.996
cdiag 264 0.000 0.0000 0.265 0.0548 0.985
cdiag1 264 0.000 0.0000 0.005 0.0010 0.526
cdiag2 264 0.000 0.0000 0.010 0.0021 0.708
cdiag3 264 0.000 0.0000 0.188 0.0388 0.787
cdiag4 264 0.000 0.0000 0.009 0.0019 0.765
c-eigvec 132 0.000 0.0000 0.147 0.0304 0.959
c-buildD 132 0.000 0.0000 0.014 0.0029 0.536
WriteDM 1 0.000 0.0000 0.008 0.0017 0.687
PostSCF 1 0.000 0.0000 1.278 0.2640 1.000
DHSCF4 1 0.000 0.0000 0.500 0.1033 0.947
dfscf 1 0.000 0.0000 0.446 0.0921 0.942
overfsm 1 0.000 0.0000 0.006 0.0012 0.833
No communications time available. Compile with -DMPI_TIMING
Definitions:
Program: Name of a time-profiled routine (or code section)
Calls: Number of profiled calls to a program
Prg.com: CPU time in communications in one program in one node
Tot.com: CPU time in communications in all progs. in one node
Prg.tot: total CPU time in one program in one node
Tot.tot: total CPU time in all programs in one node
Nod.avg: average calculation time in one program across nodes
Nod.max: maximum calculation time in one program across nodes
Calculation time: CPU time excluding communications
This diff is collapsed.
1
Al 0.000000 0.000000 0.000000
-56.3586520778081
The above number is the electronic (free)energy: -57.0690657464336
Plus the pressure : 1.359545368028931E-005 ( 0.200000000000000 GPa)
times the orbital volume (in Bohr**3): 3840.55086669502
-56.3586520778081
The above number is the electronic (free) harris energy:
-57.0690657464336
Plus the pressure : 1.359545368028931E-005 ( 0.200000000000000 GPa)
times the orbital volume (in Bohr**3): 3840.55086669502
Start of run 0.000
-------------- end of scf step 3.228
--- end of geometry step 4.518
End of run 4.861
-4.1944660179
0.000357961 -0.000000000 -0.000000000
-0.000000000 0.000357961 -0.000000000
-0.000000000 -0.000000000 0.000357961
1
1 13 -0.000000000 -0.000000000 -0.000000000 Al
SystemName Al # optional change
SystemLabel Al
#********************************************************
# Specification of atomic species and positions
#********************************************************
# Chemical species
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 13 Al
%endblock ChemicalSpeciesLabel
# UNIT CELL
LatticeConstant 4.0782 Ang #note the Co is compressed
%block LatticeVectors
0.5 0.0 0.5
0.5 0.5 0.0
0.0 0.5 0.5
%endblock LatticeVectors
# ATOMIC POSITIONS
NumberOfAtoms 1
AtomicCoordinatesFormat Ang
AtomicCoordinatesFormatOut Ang
%block AtomicCoordinatesAndAtomicSpecies
0.0000000 0.0000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
#********************************************************
# DFT options
#********************************************************
# Basis set variables
PAO.BasisType split
PAO.EnergyShift 0.02700000000 eV
%block PAO.Basis # Define Basis set
Al 3 # Species label, number of l-shells
n=3 0 2 # n, l, Nzeta
5.859 4.513
1.000 1.000
n=3 1 2 # n, l, Nzeta
6.809 5.09
1.000 1.000
n=3 2 1 # n, l, Nzeta
5.176
1.000
%endblock PAO.Basis
%block kgrid_Monkhorst_Pack
6 0 0 0.0
0 6 0 0.0
0 0 6 0.0
%endblock kgrid_Monkhorst_Pack
# General variables
ElectronicTemperature 300 K
MeshCutoff 300. Ry
xc.functional LDA # Exchange-correlation functional
xc.authors CA
SpinPolarized F
SpinOrbit F
# SCF variables
MaxSCFIterations 500 # Maximum number of SCF iter
DM.MixingWeight 0.05 # optional change
DM.Tolerance 1.0E-5
DM.UseSaveDM T # to use continuation files
DM.NumberPulay 5
SolutionMethod diagon
# Output variables
WriteMullikenPop 0
WriteBands F
SaveRho T
SaveElectrostaticPotential T
SaveTotalPotential F
WriteCoorXmol T
WriteMDXmol T
144
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