Is extraction of dipole moments from real-time TDDFT a Python command?

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Forum Regular
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2:34:30 AM PDT - Mon, Apr 27th 2015
Dear Sir

      The real-time TDDFT calculation of a molecule comprising more than twenty atoms for its
charge transfer states has been successful, but rtparse.py in the correct directory was denied in the bash when it was carried out separately . Should this and the related commands be run
with Python, or how to employ them?

      Although the calculation exhibits that the excited states energies are close to those
obtained by right-hand cr-eomccsd(t) and left-hand cr-eomccsd using NWCHEM6.5, there are
large discrepencies when compared with some cr-eomccsd(t) and cr-cc(2,3) results from GAMESS, also the reported
experimental values.
     I understand the field strength plays a role,  real-time TDDFT greatly helps understand fast
electron dynamics, and charge transfer is a challenge for computational chemistry, thus I
believe the display of the kicks is of significant importance.
Edited On 8:57:49 PM PDT - Sat, May 9th 2015 by Xiongyan21

Forum Regular
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Posts 209
8:04:51 PM PDT - Sat, May 2nd 2015
While the simultaneous compilation of NWchem6.5 and Python 3.4 seems to work on MAC 10.10.3, the following mistake appears after a rttddft calculation although there are required extracting, FFT, and ploting commands in the input. 


input_parse: unknown directive nw_rtparse.py                                                                                                                                                                                                                                                                     0

------------------------------------------------------------------------

------------------------------------------------------------------------

 current input line : 

  140: nw_rtparse.py -xdipole -px -tkick_x h2o_abs.nwo > x.dat

------------------------------------------------------------------------

------------------------------------------------------------------------

There is an error in the input file
Edited On 12:56:49 AM PDT - Sun, May 10th 2015 by Xiongyan21

Forum Regular
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Posts 209
12:59:17 AM PDT - Sun, May 10th 2015
Although " export NWCHEM_MODULES=all python" , etc are added, the following error appears when Python
commands are carried out

0:python_input is not in this build of NWChem:Received an Error in Communication
application called MPI_Abort(comm=0x84000004, -1) - process 0 .

The Python version is 3.4, and its directory is /usr/bin/PYTHON.

What is the problem here?

Forum Regular
Threads 43
Posts 209
12:59:20 AM PDT - Sun, May 10th 2015
Although " export NWCHEM_MODULES=all python" , etc are added, the following error appears when Python
commands are carried out

0:python_input is not in this build of NWChem:Received an Error in Communication
application called MPI_Abort(comm=0x84000004, -1) - process 0 .

The Python version is 3.4, and its directory is /usr/bin/PYTHON.

What is the problem here?

Forum Vet
Threads 9
Posts 1489
9:11:06 AM PDT - Mon, May 11th 2015
You need to execute
make nwchem_config
after redefining NWCHEM_MODULES

Forum Regular
Threads 43
Posts 209
3:57:04 PM PDT - Mon, May 11th 2015
Thanks very much for your answer.
In fact, I have re-installed and re-compiled NWCHEM6.5, but there is the described problem.
Edited On 4:08:13 PM PDT - Mon, May 11th 2015 by Xiongyan21

Forum Vet
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Posts 1489
9:57:56 AM PDT - Tue, May 12th 2015
Please try the following
cd $NWCHEM_TOP/src
make nwchem_config NWCHEM_MODULES="all python"
cd python
make
cd ..
make link

Forum Regular
Threads 43
Posts 209
10:45:22 PM PDT - Tue, May 12th 2015
Thanks very much for your help.
The following error message appears after the input of "make"

touch include_stamp
gfortran -c -fdefault-integer-8 -Warray-bounds -g -fno-aggressive-loop-optimizations -I. -I/usr/local/PTYTHON-3.4/include/python3.4 -I/usr/local/PTYTHON-3.4/include -I/usr/local/PTYTHON-3.4/Include -I/usr/local/PTYTHON-3.4 -I/$NWCHEM_TOP/src/include -I/users/$NWCHEM_TOP/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG python_input.F
Warning: Nonexistent include directory "/usr/local/PTYTHON-3.4/include/python3.4"
Warning: Nonexistent include directory "/usr/local/PTYTHON-3.4/include"
Warning: Nonexistent include directory "/usr/local/PTYTHON-3.4/Include"
Warning: Nonexistent include directory "/usr/local/PTYTHON-3.4"
cc -c -I. -I/usr/local/PTYTHON-3.4/include/python3.4 -I/usr/local/PTYTHON-3.4/include -I/usr/local/PTYTHON-3.4/Include -I/usr/local/PTYTHON-3.4 -I/$NWCHEM_TOP/src/include -I/$NWCHEM_TOP/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DMPICH_NO_ATTR_TYPE_TAGS -g -o task_python.o task_python.c
task_python.c:7:10: fatal error: 'Python.h' file not found
  1. include <Python.h>

1 error generated.
make***
Edited On 4:27:51 AM PDT - Wed, May 13th 2015 by Xiongyan21

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Posts 24
7:02:45 AM PDT - Wed, May 13th 2015
Quote:Xiongyan21 May 10th 12:59 am

The Python version is 3.4, and its directory is /usr/bin/PYTHON.

What is the problem here?


The actual python home is /usr/lib/python3.4 or /usr/lib64/python3.4

PYTHONHOME is /usr/local, should be /usr

export PYTHONHOME=/usr
export PYTHONVERSION=3.4
export PYTHONLIBTYPE=so

If this doesn't work, you may need to hand edit the library path in makefile.h following
ifdef USE_PYTHON64

Forum Regular
Threads 43
Posts 209
6:06:00 AM PDT - Thu, May 14th 2015
Thanks very much for your help.

This time the error message becomes

Warning: Nonexistent include directory "/usr/include/python3.4"
Warning: Nonexistent include directory "/usr/include"
Warning: Nonexistent include directory "/usr/Include"
cc -c -I. -I/usr/include/python3.4 -I/usr/include -I/usr/Include -I/usr -I/$NWCHEM_TOP/src/include -I-I/$NWCHEM_TOP/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DMPICH_NO_ATTR_TYPE_TAGS -g -o task_python.o task_python.c
task_python.c:7:10: fatal error: 'Python.h' file not found
  1. include <Python.h>
        ^
1 error generated.
make[1]: *** [/$NWCHEM_TOP/src/lib/MACX64/libnwpython.a(task_python.o)] Error 1
Edited On 4:58:07 AM PDT - Fri, May 15th 2015 by Xiongyan21

Forum Vet
Threads 9
Posts 1489
9:41:35 AM PDT - Thu, May 14th 2015
NWChem not compatible with Python 3.x
The Python interface of NWChem is not compatible with Python 3.x.
It only works with Python version 2.x

Forum Regular
Threads 43
Posts 209
4:55:36 AM PDT - Fri, May 15th 2015
Thanks a lot for your help.
The addition of Python2.7 into MAC OS X 10.10.3 still encounters the following error
...
Warning: Nonexistent include directory "/usr/include/python2.7"
Warning: Nonexistent include directory "/usr/include"
Warning: Nonexistent include directory "/usr/Include"
cc -c -I. -I/usr/include/python2.7 -I/usr/include -I/usr/Include -I/usr -I/$NWCHEM_TOP/src/include -I/$NWCHEM_TOP/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DMPICH_NO_ATTR_TYPE_TAGS -g -o task_python.o task_python.c
task_python.c:7:10: fatal error: 'Python.h' file not found
  1. include <Python.h>
        ^
1 error generated.
make[1]: *** [/$NWCHEM_TOP/lib/MACX64/libnwpython.a(task_python.o)] Error 1
make: *** [libraries] Error 1

Forum Regular
Threads 43
Posts 209
5:13:01 AM PDT - Fri, May 15th 2015
There are two errors in the GNUmakefile although I have followed Dr Drhaney' s suggestion

  1. $Id: GNUmakefile 19695 2010-10-29 16:51:02Z d3y133 $


LIBRARY = libnwpython.a

OBJ = python_input.o task_python.o nwchem_wrap.o nw_inp_from_string.o

ifndef PYTHONHOME
error:
@echo Must define PYTHONHOME and PYTHONVERSION to build with Python
@exit 1
endif

  1. Under WIN32 only need to define PYTHONHOME
ifndef PYTHONVERSION
error1:
@echo Must define PYTHONHOME and PYTHONVERSION to build with Python
@exit 1
endif


LIB_INCLUDES = -I$(PYTHONHOME)/include/python$(PYTHONVERSION) -I$(PYTHONHOME)/include -I$(PYTHONHOME)/Include -I$(PYTHONHOME)


include ../config/makefile.h
include ../config/makelib.h
Edited On 5:20:04 AM PDT - Fri, May 15th 2015 by Xiongyan21

Forum Vet
Threads 9
Posts 1489
9:54:33 AM PDT - Fri, May 15th 2015
If the directory
/usr/include/python2.7
is missing, this probably means that python 2.7 is either missing or it was not installed under /usr.

Could you please send the output of the following commands for your python 2.7 installation?

python-config --prefix
python-config --includes
python --version


The output of the commandpython-config --prefix should be used for PYTHONHOME

Quote:Xiongyan21 May 15th 3:55 am
Thanks a lot for your help.
The addition of Python2.7 into MAC OS X 10.10.3 still encounters the following error
...
Warning: Nonexistent include directory "/usr/include/python2.7"
Warning: Nonexistent include directory "/usr/include"
Warning: Nonexistent include directory "/usr/Include"
cc -c -I. -I/usr/include/python2.7 -I/usr/include -I/usr/Include -I/usr -I/$NWCHEM_TOP/src/include -I/$NWCHEM_TOP/src/tools/install/include -DMACX -DEXT_INT -DGFORTRAN -DGCC4 -DGCC46 -DPARALLEL_DIAG -DMPICH_NO_ATTR_TYPE_TAGS -g -o task_python.o task_python.c
task_python.c:7:10: fatal error: 'Python.h' file not found
  1. include <Python.h>
        ^
1 error generated.
make[1]: *** [/$NWCHEM_TOP/lib/MACX64/libnwpython.a(task_python.o)] Error 1
make: *** [libraries] Error 1

Forum Regular
Threads 43
Posts 209
10:18:01 AM PDT - Fri, May 15th 2015
Thanks a lot.

python-config --prefix
/Library/Frameworks/Python.framework/Versions/2.7

python-config --include
-I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7

python --version
Python 2.7.9


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