Hi,
For example, If you have 10 atoms, you can split them into two or more
different calculation by just changing MD.FCfirst and MD.FClast and keep
other part same.Than combine two calculation.FC files into one
calculation.FC file.
first calculation
MD.FCfirst 1
MD.FClast
I tried increasing k-points to 4,6, and 8, but the results is similar,
monoclinic structure changed to orthorhombic one. I will try to look
into pseudopotential for oxygen.
Thanks,
Tao
On 2018-05-17 10:23, T. Liu wrote:
Dear all,
I made a test on CuO (monoclinic beta = 99 expt
Dear all,
I made a test on CuO (monoclinic beta = 99 expt.), it accomplished but
the structure changed into an orthorhombic one (beta = 90). Does it mean
that the pseudopotential or/and basis set of Cu has some problems or
anything else? I also tried use 3p of Cu as semicore, but it goes to
Dear All,
After using Vibra to get the vibrational frequency, I can get such a
file called SystemLabel.vectors, and there are many coordinates (or I
may call them vectors) in the file as following,
k= 0.000.000.00
Eigenvector = 1
Frequency=
Dear All
I am working on a FC calculation on a large system. I know that we can
split the calculation over every atoms in the unit cell. But in my case
the FC calculation stop at the 6th step because of the walltime, and I
don't want to repeat the previous 5 steps with more CPU cores again
GMT+02:00 T. Liu <tl...@cam.ac.uk>:
Dear Nick,
Thanks for your help.
I compiled it again without "~", It works!
Instead, I met an old error message which I have already posted
before, but haven't got an answer. There is no DM file in the
folder.
the bottom of output file
Sett
tor, from the output you provide SIESTA is enabled
in parallel mode.
2016-10-18 14:41 GMT+02:00 T. Liu <tl...@cam.ac.uk>:
Dear Nick,
Thanks for your reply.
it is
mpirun -ppn $mpi_tasks_per_node -np $np $application $options
translated as
mpirun -ppn 16 -np 16
/home/tl439/~siesta-mai
nk/Obj/siesta <
h2o.relax.fdf > h2o.relax.out
it doesn't work neither.
I used same execution command for siesta 4.0, it works.
Regards,
Tao
On 2016-10-18 13:13, Nick Papior wrote:
Please show us your execution command line.
2016-10-18 14:08 GMT+02:00 T. Liu <tl...@cam.ac.uk>
-lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential
-lmkl_blacs_intelmpi_lp64 -lpthread -lm
PARALLEL version
Could you suggest what to do please?
Regards,
Tao
On 2016-10-14 12:18, T. Liu wrote:
Dera Nick,
Thanks for your help. It works by adding .c and using latest SCALAPCK
Dear all,
I met same error by siesta trunk 572, and there is no DM file. here is
my .fdf
SystemName H2O
SystemLabel H2O
NumberOfSpecies 2
NumberOfAtoms 3
%block ChemicalSpeciesLabel
11 H
28 O
%endblock ChemicalSpeciesLabel
LatticeConstant 1.0 Ang
%block LatticeVectors
Dera Nick,
Thanks for your help. It works by adding .c and using latest SCALAPCK.
Regards,
Tao
On 2016-10-14 11:40, Nick Papior wrote:
Try add .c to the SUFFIXES list.
2016-10-14 12:32 GMT+02:00 T. Liu <tl...@cam.ac.uk>:
Dear all,
I can compile 4.0 with the following arc
Dear all,
I can compile 4.0 with the following arch.make
arch.make
#
# Copyright (C) 1996-2016 The SIESTA group
# This file is distributed under the terms of the
# GNU General Public License: see COPYING in the top directory
# or
Dear All,
I think I found what's wrong.
the input file for vibra should be the file to build supercell, I used
supercell coordinates in the vibra input. After I changed it to unit
cell which was used for fcbuild, it works. Sorry about that.
Regards,
Tao
On 2016-07-28 12:44, T. Liu wrote
calculate the .FC in four parts and then 'cat 1.FC 2.FC 3.FC 4.FC
> H2O.FC' after deleting the first row of 2.FC 3.FC 4.FC
Could anyone suggest what's wrong with this calculation. Thanks.
Regards,
Tao
On 2016-07-28 11:49, T. Liu wrote:
Dear All,
I am using Vibra to calculate the Phonon freque
Dear All,
I am using Vibra to calculate the Phonon frequency for ice (supercell
includes 648 atoms). But meet a short error 'Killed'
Here is how I did it, Please suggest me what to do.
Starting from ice unit cell (24 atoms), use fcbuild build a supercell
including 24*3*3*3 = 648 atoms
Thanks, Nick.
On 2016-07-27 08:31, Nick Papior wrote:
Currently you cannot perform supercell expansions using off-diagonal
components.
2016-07-27 9:23 GMT+02:00 T. Liu <tl...@cam.ac.uk>:
Dear All,
I am trying to use 'supercell' block to make a
2 0 1
0 1 0
0 0 2
supercell, but Siesta s
Dear All,
I am trying to use 'supercell' block to make a
2 0 1
0 1 0
0 0 2
supercell, but Siesta stopped and showed that
Not safe to use non-diagonal supercells
Stopping Program from Node:0
Program aborted. Backtrace:
#0 0x10e968729
#1 0x10e9693a4
#2 0x10ea3e7a8
#3 0x10da4a74a
#4
Dear All,
Is it possible calculate the inertia momentum of the molecule along the
unit vectors or x,y,z axis and write the data into output file? Thanks.
Regards,
Tao
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