From NWChem
Viewed 402 times, With a total of 23 Posts
-
Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
|
|
|
Forum Vet
Threads 3
Posts 835
|
|
| 11:00:32 AM PDT - Fri, May 15th 2015 |
|
Try the following
export PYTHONHOME=/Library/Frameworks/Python.framework/Versions/2.7
export PYTHONVERSION=2.7
|
|
|
|
|
|
Gets Around
Threads 22
Posts 79
|
|
| 9:09:29 PM PDT - Fri, May 15th 2015 |
|
Thanks a lot. This time NWCHEM6.5 has been successfully built, but still there is error perhaps associated with the input file
NWChem Python program
---------------------
nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat
nw_rtparse.py -xdipole -py -tkick_y h2o_abs.nwo > y.dat
nw_rtparse.py -xdipole -pz -tkick_z h2o_abs.nwo > z.dat
fft1d -d50 -z -p50000 <x.dat | rotate_fft > xw.dat
fft1d -d50 -z -p50000 <y.dat | rotate_fft > yw.dat
fft1d -d50 -z -p50000 <z.dat | rotate_fft > zw.dat
nw_rtparse -xdipole -tkickx -px | fft1d > xw.dat
nw_rtparse -xdipole -tkicky -py | fft1d > yw.dat
nw_rtparse -xdipole -tkickz -pz | fft1d > zw.dat
paste xw.dat yw.dat zw.dat > sw.dat
gnuplot> plot "sw.dat" u ($1*27.2114) : ($1*abs($3+$7+$11))
------------------------------------------------------------------------
python failed 0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
157: task python
------------------------------------------------------------------------
------------------------------------------------------------------------
This type of error is most commonly associated with calculations not reaching convergence criteria
------------------------------------------------------------------------
For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation
The bash exhibits
File "nwchem.py", line 1
nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat
^
SyntaxError: invalid syntax
File "nwchem.py-1", line 1
nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat
File "nwchem.py-2", line 1
nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat
^
SyntaxError: ^
SyntaxError: invalid syntax
invalid syntax
0:python failed:Received an Error in Communication
application called MPI_Abort(comm=0x84000004, -1) - process 0
For further details see manual section:
=======================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 364 RUNNING AT
= EXIT CODE: 255
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
The input after the real time TDDFT is
python
nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat
nw_rtparse.py -xdipole -py -tkick_y h2o_abs.nwo > y.dat
nw_rtparse.py -xdipole -pz -tkick_z h2o_abs.nwo > z.dat
fft1d -d50 -z -p50000 <x.dat | rotate_fft > xw.dat
fft1d -d50 -z -p50000 <y.dat | rotate_fft > yw.dat
fft1d -d50 -z -p50000 <z.dat | rotate_fft > zw.dat
nw_rtparse -xdipole -tkickx -px | fft1d > xw.dat
nw_rtparse -xdipole -tkicky -py | fft1d > yw.dat
nw_rtparse -xdipole -tkickz -pz | fft1d > zw.dat
paste xw.dat yw.dat zw.dat > sw.dat
gnuplot> plot "sw.dat" u ($1*27.2114) : ($1*abs($3+$7+$11))
end
task python
|
|
Edited On 3:22:45 AM PDT - Sat, May 16th 2015 by Xiongyan21
|
|
|
|
|
|
Clicked A Few Times
Threads 2
Posts 7
|
|
| 7:25:07 AM PDT - Sat, May 16th 2015 |
|
All those commands are to be run from the command line, not inside an nwchem input file python block.
fft1d is a MatLab or octave script and only needs the file name as an argument, i.e.,
octave -q fft1d.m x.dat > xw.dat
...unless you have explicitly set your desktop environment to execute .m files using octave.
There is more information starting at page 159 in the user manual available at
http://www.nwchem-sw.org/images/NWChem6.5_Documentation.pdf
-drh
|
|
|
|
|
|
Gets Around
Threads 22
Posts 79
|
|
| 5:13:01 AM PDT - Sun, May 17th 2015 |
|
Thanks a lot for your explanation.
If commands nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat, nw_rtparse.py -xdipole -py -tkick_y h2o_abs.nwo > y.dat, and nw_rtparse.py -xdipole -pz -tkick_z h2o_abs.nwo > z.dat are typed in the bash, the following error message appears although the directory of contrib/parsers is entered:
nw_rtparse.py: command not found
|
|
Edited On 5:17:04 AM PDT - Sun, May 17th 2015 by Xiongyan21
|
|
|
|
|
|
Clicked A Few Times
Threads 2
Posts 7
|
|
| 10:26:21 AM PDT - Sun, May 17th 2015 |
|
Quote:Xiongyan21 May 17th 5:13 amIf commands ... are typed in the bash, the following error message appears although the directory of contrib/parsers is entered:
nw_rtparse.py: command not found
If you are already in $NWCHEM_TOP/contrib/parsers, the command becomes:
./nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat
Executable files in your current working directory need to be specified with a leading ./,
otherwise the system will only search in the PATH directories.
-drh
|
|
|
|
|
|
Gets Around
Threads 22
Posts 79
|
|
| 7:11:37 PM PDT - Sun, May 17th 2015 |
|
Thanks a lot for your explanation.
The permission of " ./nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat " is denied
in the bash although the directory of contrib/parsers is entered.
|
|
|
|
|
|
Clicked A Few Times
Threads 2
Posts 7
|
|
| 10:28:35 AM PDT - Mon, May 18th 2015 |
|
Quote:Xiongyan21 May 17th 7:11 pmThanks a lot for your explanation.
The permission of " ./nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat " is denied
in the bash although the directory of contrib/parsers is entered.
You must study how to set Linux file permissions or flags, and the different ways of invoking python scripts.
-drh
|
|
|
|
|
|
Gets Around
Threads 22
Posts 79
|
|
| 3:55:02 PM PDT - Mon, May 18th 2015 |
|
| Does it mean that the commands cannot be carried out on MAC OS X?
|
|
|
|
|
|
Gets Around
Threads 11
Posts 98
|
|
| 4:16:42 PM PDT - Mon, May 18th 2015 |
|
No, it means that the Python file is not marked executable.
Try
python nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat
instead.
|
|
|
AWC's:
2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC
