[lammps-users] problem with dump xyz

-- quote --
i am using the command:
dump 1 all xyz 1000 diamante.xyz

and the format:
dump 1 all atoms 1000 diamante.xyz
dump_modify 1 header xyz

for obtain a serious of xyz images with lammps, but this command line don't run, someone can tell my what are making bad?.
thank you.
-- end quote --

"header" is not a keyword of the dump_modify command. Revisit the page http://lammps.sandia.gov/doc/dump_modify.html

hi

i am using the command:
dump 1 all xyz 1000 diamante.xyz

and the format:
dump 1 all atoms 1000 diamante.xyz
dump_modify 1 header xyz

for obtain a serious of xyz images with lammps, but this
command line don't run, someone can tell my what are
making bad?.
thank you.
-- end quote --

"header" is not a keyword of the dump_modify
command. Revisit the page
http://lammps.sandia.gov/doc/dump_modify.html

ok, but the first command:
dump 1 all xyz 1000 diamante.xyz

i think are good becouse in the manual specify xyz how a style, but when launch the script tell that style don't exist. (what's the problem with this command?).

the other format with dump_modify are used in some documents, but i assume that are a previous version format.

thanks.

If I add this line to bench/in.lj

dump 1 all xyz 1000 diamante.xyz

it works fine. What error are you getting?

Steve

Hi, steve and all,

I want to comple LAMMPs with MEAM.

Fistly, according to the manual, I used ifort compiler to create the /lib/meam/ libaray. And then use the following Makefile for the MEAM. Where is the wrong thing? Note that I successfully compiled it without MEAM.
I remember Alex and steve said that it is the problem with linking with c++ and fortran code. But I need more detailed suggestion.

Thanks in advance!

AC

…/…/lib/meam/libmeam.a(meam_setup_done.o): In function zbl_': meam_setup_done.F:(.text+0x1413): undefined reference to _svml_exp2’
…/…/lib/meam/libmeam.a(meam_setup_done.o): In function get_zij2_': meam_setup_done.F:(.text+0x14b3): undefined reference to for_cpstr’
meam_setup_done.F:(.text+0x14da): undefined reference to for_cpstr' meam_setup_done.F:(.text+0x1501): undefined reference to for_cpstr’
meam_setup_done.F:(.text+0x1528): undefined reference to for_cpstr' meam_setup_done.F:(.text+0x154f): undefined reference to for_cpstr’
meam_setup_done.F:(.text+0x15ae): undefined reference to __powr8i4' ../../lib/meam/libmeam.a(meam_setup_done.o): In function get_shpfcn
’:
meam_setup_done.F:(.text+0x1650): undefined reference to for_cpstr' meam_setup_done.F:(.text+0x1672): undefined reference to for_cpstr’
meam_setup_done.F:(.text+0x1694): undefined reference to for_cpstr' meam_setup_done.F:(.text+0x16cb): undefined reference to for_cpstr’
meam_setup_done.F:(.text+0x16f2): undefined reference to `for_cpstr’

The Makefile I used is :

C = mpicxx
CCFLAGS = -O -I/export/mpich2.1/include -DMPICH_IGNORE_CXX_SEEK
-DFFT_FFTW -I/export/fftw2/include -I …/…/lib/meam
-DGZIP
DEPFLAGS = -M
LINK = mpif90
LINKFLAGS = -O -L/export/mpich2.1/lib -L/export/fftw2/lib
-L …/…/lib/meam -L/export/intel/fce/10.0.023/lib (this is my intel fortran compiler)

USRLIB = -lfftw -lmpich -lmeam
SYSLIB = -lstdc++
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size

Hi, steve and all,

I want to comple LAMMPs with MEAM.

Fistly, according to the manual, I used ifort compiler to create the
/lib/meam/ libaray. And then use the following Makefile for the
MEAM. Where is the wrong thing? Note that I successfully compiled it
without MEAM. I remember Alex and steve said that it is the problem
with linking with c++ and fortran code. But I need more detailed
suggestion.

does your mpif90 call ifort or some other compiler?
you have to make sure that you compile libmeam.a with
the same compiler as LAMMPS. if you are uncertain,
you can try using mpif90 to compile libmeam.a instead
of ifort.

cheers,
  
    axel.

Thanks in advance!

AC

../../lib/meam/libmeam.a(meam_setup_done.o): In function `zbl_':meam_setup_done.F:(.text+0x1413): undefined reference to `__svml_exp2'../../lib/meam/libmeam.a(meam_setup_done.o): In function `get_zij2_':meam_setup_done.F:(.text+0x14b3): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x14da): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x1501): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x1528): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x154f): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x15ae): undefined reference to `__powr8i4'../../lib/meam/libmeam.a(meam_setup_done.o): In function `get_shpfcn_':meam_setup_done.F:(.text+0x1650): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x1672): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x1694): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x16cb): undefined reference to `for_cpstr'meam_setup_done.F:(.text+0x16f2!

): undefined reference to `for_cpstr'....

....

....

The Makefile I used is :

C = mpicxx
CCFLAGS = -O -I/export/mpich2.1/include -DMPICH_IGNORE_CXX_SEEK \
-DFFT_FFTW -I/export/fftw2/include -I../../lib/meam \
-DGZIP
DEPFLAGS = -M
LINK = mpif90
LINKFLAGS = -O
-L/export/mpich2.1/lib -L/export/fftw2/lib \ -L ../../lib/meam
-L/export/intel/fce/10.0.023/lib (this is my intel fortran compiler)

USRLIB = -lfftw -lmpich -lmeam
SYSLIB = -lstdc++
ARCHIVE = ar
ARFLAGS = -rc
SIZE =

size

does your mpif90 call ifort or some other compiler?
you have to make sure that you compile libmeam.a with
the same compiler as LAMMPS. if you are uncertain,
you can try using mpif90 to compile libmeam.a instead
of ifort.

Thanks for you reply. But it is not lucky to get this problem fixed yet with your recommandation. confusing…

AJ

> does your mpif90 call ifort or some other compiler?> you have to
> make sure that you compile libmeam.a with> the same compiler as
> LAMMPS. if you are uncertain,> you can try using mpif90 to
> compile libmeam.a instead> of ifort.

Thanks for you reply. But it is not lucky to get this problem fixed yet with your recommandation. confusing....

luck has nothing to do with it. if you do it properly,
it will work. this is very difficult to diagnose over the
internet (particularly, "it doesn't work" is hard to debug).
your best shot is to try and find somebody locally to help
you with this, that is an expert on compilers and libraries.

cheers,
    axel.