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Commit c6d2fa7a authored by Doak, Peter W's avatar Doak, Peter W
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removing retired systems

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OIC/VASP/INCAR deleted 100644 → 0
View file @ abdaaa99
System = CeO2 : fcc
ISTART = 0
ICHARG = 2
PREC=Normal
ALGO=Fast
ENCUT = 400.00
EDIFF = 0.1E-04
LREAL=Auto
LCHARG = .FALSE.
LWAVE = .FALSE.
LDAU = .TRUE. #Switch on the L(S)DA+U
LDAUTYPE = 2 #Dudarev's approach
LDAUL = 3 -1 #Ce and O LDAUL, LDAUU and LDAUJ must be specified for all atomic species
LDAUU = 5.5 0 #Ce and O
LDAUJ = 0 0 #Ce and O
LMAXMIX=6
ISMEAR=0
SIGMA=0.1
NPAR=2
OIC/VASP/KPOINTS deleted 100644 → 0
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K-Points
0
Monkhorst Pack
1 1 1
0 0 0
OIC/VASP/POSCAR deleted 100644 → 0
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Ce O : CeO2 fcc (110)-Surf.: 2x3-cell
5.401
2.121320344 0.000000000 0.000000
0.000000000 2.000000000 0.000000
0.000000000 0.000000000 4.017767
36 72
Cart
0.00000000 0.00000000 0.00000000 T T T
0.00000000 1.00000000 0.00000000 T T T
0.70710677 0.00000000 0.00000000 T T T
0.70710677 1.00000000 0.00000000 T T T
1.41421354 0.00000000 0.00000000 T T T
1.41421354 1.00000000 0.00000000 T T T
0.35355338 -0.50000000 0.35355338 T T T
0.35355338 0.50000000 0.35355338 T T T
1.06066012 -0.50000000 0.35355338 T T T
1.06066012 0.50000000 0.35355338 T T T
1.76776695 -0.50000000 0.35355338 T T T
1.76776695 0.50000000 0.35355338 T T T
0.00000000 0.00000000 0.70710677 T T T
0.00000000 1.00000000 0.70710677 T T T
0.70710677 0.00000000 0.70710677 T T T
0.70710677 1.00000000 0.70710677 T T T
1.41421354 0.00000000 0.70710677 T T T
1.41421354 1.00000000 0.70710677 T T T
0.35355338 -0.50000000 1.06066012 T T T
0.35355338 0.50000000 1.06066012 T T T
1.06066012 -0.50000000 1.06066012 T T T
1.06066012 0.50000000 1.06066012 T T T
1.76776695 -0.50000000 1.06066012 T T T
1.76776695 0.50000000 1.06066012 T T T
0.00000000 0.00000000 1.41421354 T T T
0.00000000 1.00000000 1.41421354 T T T
0.70710677 0.00000000 1.41421354 T T T
0.70710677 1.00000000 1.41421354 T T T
1.41421354 0.00000000 1.41421354 T T T
1.41421354 1.00000000 1.41421354 T T T
0.35355335 -0.50000000 1.76776695 T T T
0.35355335 0.50000000 1.76776695 T T T
1.06066012 -0.50000000 1.76776695 T T T
1.06066012 0.50000000 1.76776695 T T T
1.76776695 -0.50000000 1.76776695 T T T
1.76776695 0.50000000 1.76776695 T T T
-0.35355338 -0.25000000 0.00000000 T T T
-0.35355338 0.75000000 0.00000000 T T T
0.35355338 -0.25000000 0.00000000 T T T
0.35355338 0.75000000 0.00000000 T T T
1.06066012 -0.25000000 0.00000000 T T T
1.06066012 0.75000000 0.00000000 T T T
-0.35355338 0.25000000 0.00000000 T T T
-0.35355338 1.25000000 0.00000000 T T T
0.35355338 0.25000000 0.00000000 T T T
0.35355338 1.25000000 0.00000000 T T T
1.06066012 0.25000000 0.00000000 T T T
1.06066012 1.25000000 0.00000000 T T T
0.00000000 -0.75000000 0.35355338 T T T
0.00000000 0.25000000 0.35355338 T T T
0.70710677 -0.75000000 0.35355338 T T T
0.70710677 0.25000000 0.35355338 T T T
1.41421354 -0.75000000 0.35355338 T T T
1.41421354 0.25000000 0.35355338 T T T
0.00000000 -0.25000000 0.35355338 T T T
0.00000000 0.75000000 0.35355338 T T T
0.70710677 -0.25000000 0.35355338 T T T
0.70710677 0.75000000 0.35355338 T T T
1.41421354 -0.25000000 0.35355338 T T T
1.41421354 0.75000000 0.35355338 T T T
-0.35355335 -0.25000000 0.70710677 T T T
-0.35355335 0.75000000 0.70710677 T T T
0.35355341 -0.25000000 0.70710677 T T T
0.35355341 0.75000000 0.70710677 T T T
1.06066012 -0.25000000 0.70710677 T T T
1.06066012 0.75000000 0.70710677 T T T
-0.35355335 0.25000000 0.70710677 T T T
-0.35355335 1.25000000 0.70710677 T T T
0.35355341 0.25000000 0.70710677 T T T
0.35355341 1.25000000 0.70710677 T T T
1.06066012 0.25000000 0.70710677 T T T
1.06066012 1.25000000 0.70710677 T T T
0.00000000 -0.75000000 1.06066012 T T T
0.00000000 0.25000000 1.06066012 T T T
0.70710677 -0.75000000 1.06066012 T T T
0.70710677 0.25000000 1.06066012 T T T
1.41421354 -0.75000000 1.06066012 T T T
1.41421354 0.25000000 1.06066012 T T T
0.00000000 -0.25000000 1.06066012 T T T
0.00000000 0.75000000 1.06066012 T T T
0.70710677 -0.25000000 1.06066012 T T T
0.70710677 0.75000000 1.06066012 T T T
1.41421354 -0.25000000 1.06066012 T T T
1.41421354 0.75000000 1.06066012 T T T
-0.35355341 -0.25000000 1.41421354 T T T
-0.35355341 0.75000000 1.41421354 T T T
0.35355335 -0.25000000 1.41421354 T T T
0.35355335 0.75000000 1.41421354 T T T
1.06066012 -0.25000000 1.41421354 T T T
1.06066012 0.75000000 1.41421354 T T T
-0.35355341 0.25000000 1.41421354 T T T
-0.35355341 1.25000000 1.41421354 T T T
0.35355335 0.25000000 1.41421354 T T T
0.35355335 1.25000000 1.41421354 T T T
1.06066012 0.25000000 1.41421354 T T T
1.06066012 1.25000000 1.41421354 T T T
0.00000000 -0.75000000 1.76776695 T T T
0.00000000 0.25000000 1.76776695 T T T
0.70710677 -0.75000000 1.76776695 T T T
0.70710677 0.25000000 1.76776695 T T T
1.41421354 -0.75000000 1.76776695 T T T
1.41421354 0.25000000 1.76776695 T T T
0.00000000 -0.25000000 1.76776695 T T T
0.00000000 0.75000000 1.76776695 T T T
0.70710677 -0.25000000 1.76776695 T T T
0.70710677 0.75000000 1.76776695 T T T
1.41421354 -0.25000000 1.76776695 T T T
1.41421354 0.75000000 1.76776695 T T T
OIC/VASP/POTCAR deleted 100644 → 0
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OIC/VASP/vasp_job.pbs deleted 100644 → 0
View file @ abdaaa99
#!/bin/bash
##PBS -S /bin/bash
#PBS -m be
#PBS -M yourmail@ornl.gov
#PBS -N vasp_test
#PBS -q cnms14q
#PBS -l nodes=3:ppn=32
#PBS -l walltime=24:00:00
#PBS -W x=NACCESSPOLICY:SINGLEJOB
source /opt/modules/3.1.6/init/bash
#cd $GLOBAL_SCRATCH
cd $PBS_O_WORKDIR
export MODULEPATH=$MODULEPATH:/projects/cnms/modules
module load vasp
export OMP_NUM_THREADS=1
cd $PBS_O_WORKDIR
#this can be useful to see from outside shells
cat $PBS_NODEFILE >pbs_nodefile
cores_per_node=32
wcr=($(wc pbs_nodefile))
count=${wcr[0]}
awk -v count=$count -v cpn=$cores_per_node 'BEGIN { a= 0; r=0; cores=count/2; prev_node="" }; { if (a < cpn) { print "rank " r "=" $1 " slot=" a; r = r + 1; a = a + 2; prev_node=$1 } else { if (r < cores && prev_node != $1 ) {a = 0; print "rank " r "=" $1 " slot=" a ; r = r + 1; a = a + 2} }}' pbs_nodefile > rankfile
#VASP runs including significant communication especially for SCALAPACK run
#slower than they should. Refrain from using more than ~1 cpu per atom
#past 64 or 128 cores LSCALAPACK=.FALSE.
mpirun -n $((count / 2)) -v --report-bindings -rf rankfile ${VASP_MPI_FLAGS} $VASP 2>&1 >vasp_out
OIC/lammps/in.colloid deleted 100644 → 0
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# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
create_atoms 1 box
set group all type/fraction 2 0.96 23984
set type 1 mass 9
set type 2 mass 1
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
comm_modify mode multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 &
mtk no pchain 0 tchain 1
fix 2 all enforce2d
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
OIC/lammps/lammps_pbs deleted 100644 → 0
View file @ abdaaa99
#!/bin/bash
#PBS -S /bin/bash
#PBS -m be
#PBS -M your@email
#PBS -N lammps_test
#PBS -q cnms14q
#PBS -l nodes=2:ppn=16
#PBS -l walltime=00:30:00
#PBS -W x=NACCESSPOLICY:SINGLEJOB
source /opt/modules/3.1.6/init/bash
#cd $GLOBAL_SCRATCH
cd $PBS_O_WORKDIR
export MODULEPATH=$MODULEPATH:/projects/cnms/modules
module load lammps
#echo `ls -ltr`
export OMP_NUM_THREADS=1
mpirun $LAMMPS_MPI_FLAGS $LAMMPS < in.colloid
TITAN/namd/apoa1/apoa1.namd deleted 100644 → 0
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cellBasisVector1 108.8612 0.0 0.0
cellBasisVector2 0.0 108.8612 0.0
cellBasisVector3 0.0 0.0 77.758
cellOrigin 0.0 0.0 0.0
coordinates apoa1.pdb
temperature 300
seed 74269
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
PME on
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80
structure apoa1.psf
parameters par_all22_prot_lipid.xplor
parameters par_all22_popc.xplor
exclude scaled1-4
1-4scaling 1.0
timestep 1.0
fullElectFrequency 4
numsteps 500
outputtiming 20
outputname /usr/tmp/apoa1-out
TITAN/namd/apoa1/apoa1.pdb deleted 100644 → 0
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TITAN/namd/apoa1/apoa1.psf deleted 100644 → 0
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TITAN/namd/apoa1/par_all22_popc.xplor deleted 100644 → 0
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REMARKS Additional POPC parameters guessed by Jim Phillips
REMARKS FILENAME="par_all22_popc.xplor"
ANGLE CEL1 CEL1 CTL2 48.00 124.00 ! JCP guess 3/97
ANGLE CEL1 CTL2 CTL2 32.00 112.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 CTL2 0.5000 3 0.00 ! JCP guess 3/97
DIHEDRAL HAL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 HAL 0.1200 3 0.00 ! JCP guess 3/97
TITAN/namd/apoa1/par_all22_prot_lipid.xplor deleted 100644 → 0
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TITAN/namd/apoa1/run_namd.sh deleted 100644 → 0
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#!/bin/bash
#PBS -A youracct
#PBS -N test
#PBS -q debug
#PBS -j oe
#PBS -l walltime=0:30:00
#PBS -l nodes=100
module load namd/2.12
which namd2
export MPICH_PTL_SEND_CREDITS=-1
export MPICH_MAX_SHORT_MSG_SIZE=8000
export MPICH_PTL_UNEX_EVENTS=80000
export MPICH_UNEX_BUFFER_SIZE=100M
NPROC=$((PBS_NUM_NODES))
cd $PBS_O_WORKDIR
aprun -n $NPROC -N 1 -d 8 namd2 ++ppn 7 +setcpuaffinity \
+pemap 0,2,4,6,8,10,12 +commap 14 +idlepoll +devices 0 \
apoa1.namd >& apoa1_test.log
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