Problem in modifying the subroutine

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Dear NWChem developers and users,
I am trying to modify the source code in order to a different type of field other than the ones that is specified in the subroutine: rt_tddft_exite.F.
When I tried to use “Make Install”, I got the following error.
Could you help?
Thank you very much.

Toshiharu Higuchi
Yokohama, Japan


user@pc:/$ cd /
user@pc:/$ cd /home/user/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils
user@pc:~/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils$ make
/home/user/NWChem-6.6/nwchem-6.6/bin/LINUX/depend.x -I../../include -I../../../ddscf -I/home/user/NWChem-6.6/nwchem-6.6/src/tools/install/include > dependencies
gfortran -c -m32 -march=pentium4 -mtune=pentium4 -g -O2 -g -fno-aggressive-loop-optimizations -g -O0 -I. -I../../include -I../../../ddscf -I/home/user/NWChem-6.6/nwchem-6.6/src/include -I/home/user/NWChem-6.6/nwchem-6.6/src/tools/install/include -DLINUX -DGFORTRAN -DGCC46 -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG -DDEBUG_PRINT rt_tddft_excite.F
rt_tddft_excite.F:81.35:

     call rt_tddft_update_fields (params, tt)                          
1
Warning: Dummy argument 'params' with INTENT(IN) in variable definition context (actual argument to INTENT = OUT/INOUT) at (1)
Got lock on /home/user/NWChem-6.6/nwchem-6.6/lib/LINUX/libnwdft.lock
ar r /home/user/NWChem-6.6/nwchem-6.6/lib/LINUX/libnwdft.a rt_tddft_excite.o
ranlib /home/user/NWChem-6.6/nwchem-6.6/lib/LINUX/libnwdft.a

user@pc:~/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils$ sudo make install
[sudo] password for user:

You must define NWCHEM_TOP in your environment to be the path
of the top level nwchem directory ... something like
setenv NWCHEM_TOP /msrc/home/elvis/nwchem

../../../config/makefile.h:33: *** . Stop.
user@pc:~/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils$

Forum Vet
Threads 7
Posts 1355
sudo needed?
This are the commands that you should execute to link a NWChem binary with your new changed to rt_tddft_excite.F (assuming that you have already compiled your $NWCHEM_TOP/src/ once ... is this your case?)

cd $NWCHEM_TOP/src/nwdft/rt_tddft/rtutils
make
cd $NWCHEM_TOP/src
make link

PS You see to have chosen NWCHEM_TARGET=LINUX A better option is -- if your CPU allows it -- NWCHEM_TARGET=LINUX64
Edited On 12:57:00 PM PST - Thu, Jan 19th 2017 by Edoapra

Clicked A Few Times
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Posts 12
Tkank you very much for your kind reply.
However, next sentence is difficult for me to understand.
Please tell me a little bit more detail.

(assuming that you have already compiled your $NWCHEM_TOP/src/ once ... is this your case?)


Toshiharu Higuchi
Yokohama, Japan

Forum Vet
Threads 7
Posts 1355
Please read the following webpage
http://www.nwchem-sw.org/index.php/Compiling_NWChem
The following section describes how to compile the source code to produce a binary
http://www.nwchem-sw.org/index.php/Compiling_NWChem#Building_the_NWChem_binary

Clicked A Few Times
Threads 3
Posts 12
Dear Dr. Edoapra; Forum admin,
thank you very much for your kind reply.

I have done the make & make link, based on your comments.


$ cd /home/user/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils
 make
$ cd /home/user/NWChem-6.6/nwchem-6.6/src
 make link

And I get the following log. file.
Because there is no error message, I think that it is good.
However I have no confidence.

If you have any comment, please teach me.

Thank you,

Toshiharu Higuchi
Yokohama, Japan

<< log.file >>
cf. In the parenthesis, it is English transulation of the upper sentence.

user@user-desktop:~$ cd /home/user/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils
user@user-desktop:~/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils$ make
/home/user/NWChem-6.6/nwchem-6.6/bin/LINUX64/depend.x -I../../include -I../../../ddscf -I/home/user/NWChem-6.6/nwchem-6.6/src/tools/install/include > dependencies
make: Warning: Archive '/home/user/NWChem-6.6/nwchem-6.6/lib/LINUX64/libnwdft.a' seems to have been created in deterministic mode. '!' will always be updated. Please consider passing the U flag to ar to avoid the problem.
gfortran -c -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I../../include -I../../../ddscf -I/home/user/NWChem-6.6/nwchem-6.6/src/include -I/home/user/NWChem-6.6/nwchem-6.6/src/tools/install/include -DGFORTRAN -DCHKUNDFLW -DGCC4 -DGCC46 -DEXT_INT -DLINUX -DLINUX64 -DPARALLEL_DIAG -DDEBUG_PRINT rt_tddft_excite.F
rt_tddft_excite.F:81:35:

      call rt_tddft_update_fields (params, tt)
1
Warning: Dummy argument ‘params’ with INTENT(IN) in variable definition context (actual argument to INTENT = OUT/INOUT) at (1)
make: Warning: Archive '/home/user/NWChem-6.6/nwchem-6.6/lib/LINUX64/libnwdft.a' seems to have been created in deterministic mode. 'rt_tddft_excite.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[1]: ?????? '/home/user/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils' ?????

(Into the directory '/home/user/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils')

Got lock on /home/user/NWChem-6.6/nwchem-6.6/lib/LINUX64/libnwdft.lock
ar r /home/user/NWChem-6.6/nwchem-6.6/lib/LINUX64/libnwdft.a rt_tddft_excite.o
echo /home/user/NWChem-6.6/nwchem-6.6/lib/LINUX64/libnwdft.a
/home/user/NWChem-6.6/nwchem-6.6/lib/LINUX64/libnwdft.a
make[1]: ?????? '/home/user/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils' ?????

(Out of the directory '/home/user/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils')

user@user-desktop:~/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils$



user@user-desktop:~/NWChem-6.6/nwchem-6.6/src/nwdft/rt_tddft/rtutils$ cd /
user@user-desktop:/$ cd /home/user/NWChem-6.6/nwchem-6.6/src
user@user-desktop:~/NWChem-6.6/nwchem-6.6/src$ make link
make nwchem.o stubs.o
make[1]: ?????? '/home/user/NWChem-6.6/nwchem-6.6/src' ?????

(Into the directory '/home/user/NWChem-6.6/nwchem-6.6/src')

gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/home/user/NWChem-6.6/nwchem-6.6/src/include -I/home/user/NWChem-6.6/nwchem-6.6/src/tools/install/include -DGFORTRAN -DCHKUNDFLW -DGCC4 -DGCC46 -DEXT_INT -DLINUX -DLINUX64 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/home/user/NWChem-6.6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/home/user/NWChem-6.6/nwchem-6.6/src/include -I/home/user/NWChem-6.6/nwchem-6.6/src/tools/install/include -DGFORTRAN -DCHKUNDFLW -DGCC4 -DGCC46 -DEXT_INT -DLINUX -DLINUX64 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/home/user/NWChem-6.6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: ?????? '/home/user/NWChem-6.6/nwchem-6.6/src' ?????

(Out of the directory '/home/user/NWChem-6.6/nwchem-6.6/src')

gfortran -L/home/user/NWChem-6.6/nwchem-6.6/lib/LINUX64 -L/home/user/NWChem-6.6/nwchem-6.6/src/tools/install/lib -o /home/user/NWChem-6.6/nwchem-6.6/bin/LINUX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -l64to32 -lopenblas -lpthread -lrt -lnwclapack -lnwcblas -L/usr/lib/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lrt -lm -lpthread
user@user-desktop:~/NWChem-6.6/nwchem-6.6/src$

Forum Vet
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I don't see any obvious problem

Clicked A Few Times
Threads 3
Posts 12
Thank you very much for your kind reply.
I am trying the partial recompile/relinking.
After the repeating test, I will post the results.

By the way, can I paste the figures (ie. jpg, pdf etc) in this post?

Best regard,
Toshiharu Higuchi
Yokohama, Japan

Clicked A Few Times
Threads 3
Posts 12
Thank you very much for your kind reply.
I tried the partial recompile/relinking using the “computes Hann function for windowing pulse” in rf_tddft_excite.F.
I changed the equation from hout=sin(arg)*sin(arg) to hout=sin(arg), and calculate the E-Field using the following .nw input file.
Then I executed the repeating test.
However the results were inconsistent as shown in below.
There may be something wrong.
If you have any comments, please teach me.

Best regard,
Toshiharu Higuchi
Yokohama, Japan


<<<Repeating Test>>>
[1] Step 1: original
(1-1)Equation of rt_tddft_excite.F ; hout=sin(arg) * sin(arg)
(1-2)make & make link ; Not Execute
(1-3)Result: E-Field
     Peak Field = 5.49E7 V/cm
Width = 1.26 fs

[2] Step 2:
Using the original file (Step 1 file), changed the equation and then executed the “make & make install”. I get the reasonable result.

(2-1)Equation of rt_tddft_excite.F ; hout=sin(arg)
(2-2)make & make link ; Execute
(2-3)Result: E-Field
     Peak Field = -3.35E7 V/cm
Width = 1.26 fs

[3] Step 3:
Using the Step 2 file, no change the equation and then no execution the “make & make install”. It is a repeatable test. Thus we should get a same result with Step 2. However Result was same as Step 1. Why??

(3-1)Equation of rt_tddft_excite.F ; hout=sin(arg)
(3-2)make & make link ; Not Execute
(3-3)Result: E-Field
     Peak Field = 5.89E7 V/cm
Width = 1.26 fs

[4] Step 4:
Using the Step 3 file, no change the equation and then execute the “make & make install”. It is a repeatable test. Equation is same as Step 3. Thus we should get a same result with Step 3. However Result was not same as Step 3. Why??

(4-1)Equation of rt_tddft_excite.F ; hout=sin(arg)
(4-2)make & make link ; Execute
(4-3)Result: E-Field
     Peak Field = -7.3E7 V/cm
Width = 1.26 fs


<<<Input file: H-GRH_SrcCode_170121A.nw>>>
Note: 1. means #.
        In the .nw file, I used #, however in this post # is changed 1..

title "h_grh H-GRH_SrcCode_170121A"

  1. define a simulation cell###
NWPW
 SIMULATION_CELL
cell_name h-termi-gra
boundary_conditions periodic
lattice_vectors
22.500d0 0.000d0 0.000d0
0.000d0 6.9635973d0 0.000d0
0.000d0 0.000d0 2.4869877d0
ngrid 100 31 12
END
END

  1. geometry###
geometry "system" units angstrom nocenter noautosym noautoz
   H     13.682904016    1.740899325    1.243493850    
C 14.777498488 1.740899325 1.243493850
C 15.442484477 1.740899325 0.000000000
C 16.872015021 1.740899325 0.000000000
C 17.564308380 1.740899325 1.243493850
H 18.658900000 1.740899325 1.243493850
end

set geometry "system"

basis
   H  library 3-21G
C library 3-21G
end

  1. task dft###

dft
xc pbe0
convergence energy 1e-5
iterations 300
vectors output H-GRH_SrcCode_170121A.movecs

end

  1. task dft energy

  1. dplot###
dplot
 TITLE HGRA
vectors H-GRH_SrcCode_170121A.movecs
LimitXYZ
0.0 22.5 100
0.0 6.9635973 31
0.0 2.4869877 12
spin total
gaussian
output chargedenity.cube
end

task dft
task dplot

  1. rt-tddft###

unset rt_tddft:*
rt_tddft
 tmax 400.0
dt 0.2

 field "hpulse"
type hann
polarization x
frequency 0.12
center 200.0
width 50.0
max 0.01459
spin total
end

excite "system" with "hpulse"

  1. Visualization###

 visualization
tstart 0.0
tend 400.0
treference 0.0
dplot
end

end

task dft rt_tddft

Gets Around
Threads 1
Posts 144
I was unable to reproduce the error your describe, even after making the modification to the source code that you said you made, i.e. my results were consistent between runs.

Were you getting consistent results if you repeated the same calculation before you modified the source code?

Also, please note that RT-TDDFT is implemented within the Gaussian basis set part of NWChem and not within the plane wave part of NWChem. This means that the code is ignoring the NWPW block of your input file, and your system is not being treated with periodic boundary conditions.

Clicked A Few Times
Threads 3
Posts 12
Dear Dr. Sean,
thank you very much for your kind reply.

I tried the repeat tests under no changing the source code (rt_tddft_excite.F) and *.nw input file. I could not get consistent results as shown in below.
I am troubled why such results came out.
Please help me.

Note:  
rt_tddft_excite.F = original
*.nw input file = H-GRH_SrcCode_170121A.nw. This file was attached in Jan. 25th
2017 this Post.

<< Results >>
[1]Step 1: original
 Peak E-Field = - 7.250470266E7 (V/cm)

[2]Step 2: different from Step 1
 Peak E-Field = - 6.146795755E7 (V/cm)

[3]Step 3: equal to Step 1
 Peak E-Field = - 7.250470266E7 (V/cm)

[4]Step 4: equal to Step 1
 Peak E-Field = - 7.250470266E7 (V/cm)

[5]Step 5: Field was changed from minus value to plus value.
 Peak E-Field = + 7.386817508E7 (V/cm)

Gets Around
Threads 1
Posts 144
My guess is that there is trouble with your build. I would first try running some of the test calculations in $NWCHEM_TOP/QA/tests/ (there are hundreds in there, just pick a few) and see if you get the same results as the reference output. Also what is your build environment (all of the environment variables that you set when compiling)?

Clicked A Few Times
Threads 3
Posts 12
Dear Dr. Sean,
Thank you very much for your kind reply.
I tried three test calculations in $NWCHEM_TOP/QA/tests. Results are as follows. I did not get the same results as the reference output.
Regarding the build environment, please refer following “.bashrc”.
Please help me.
Best regards,

Toshiharu Higuchi
Yokohama, Japan


<<< test calculations >>>
[1] rt_tddft_cytosine_cam_cdfit: Test values of dipole moment are nearly equal to the references.
[2] rt_tddft_dimer_charge: Z- dipole moment of test value is nearly equal to the reference. But, X, Y-dipole moment of test value is completely different with the reference.
[3] rt_tddft_tcne_spinkick: The values of dipole moment of tests are close to the references. But they are not equal.

<<< details >>>
[1] rt_tddft_cytosine_cam_cdfit:
Test values of dipole moment are nearly equal to the references.
<< Reference >>
<rt_tddft>: 0.60000 2.256531542719E+000 -7.747013208988E-001 1.145943021330E+000 # Dipole moment [system]

<< Test result >>
<rt_tddft>: 0.60000 2.256531323402E+000 -7.747013812446E-001 1.145942918391E+000 # Dipole moment [system]


[2] rt_tddft_dimer_charge:
Z- dipole moment of test value is nearly equal to the reference. But, X, Y-dipole moment of test value is completely different with the reference.
<< Reference >>
<rt_tddft>: 49.60000 -4.623201778006E-013 -9.465024909606E-017 2.426376900976E-003 # Dipole moment [bottom] (alpha spin)
<rt_tddft>: 49.60000 -2.456440541428E-013 7.698925710996E-017 -7.189200855800E-003 # Dipole moment [bottom] (beta spin)
<rt_tddft>: 49.60000 -7.075184080101E-013 -1.766099198610E-017 -4.762823954824E-003 # Dipole moment [bottom] (total spin)
<rt_tddft>: 49.60000 9.148389511215E-015 1.972141114059E-016 2.616569971847E+000 # Dipole moment [top] (alpha spin)
<rt_tddft>: 49.60000 2.525029610314E-014 -5.034380895189E-017 3.572964500638E+000 # Dipole moment [top] (beta spin)
<rt_tddft>: 49.60000 3.462074377181E-014 1.468703024540E-016 -1.369369481835E+000 # Dipole moment [top] (total spin)
<rt_tddft>: 49.60000 -3.442750641861E-013 1.390766226378E-016 2.912826293045E+000 # Dipole moment [dimer] (alpha spin)
<rt_tddft>: 49.60000 -1.899785667323E-013 4.505618980374E-017 3.762160244963E+000 # Dipole moment [dimer] (beta spin)
<rt_tddft>: 49.60000 -5.335493331871E-013 1.841328124416E-016 -8.839174163122E-001 # Dipole moment [dimer]

<< Test Result >>
<rt_tddft>: 49.60000 -1.087889007855E-009 5.515256629233E-011 2.426602442809E-003 # Dipole moment [bottom] (alpha spin)
<rt_tddft>: 49.60000 9.568586239106E-011 -4.527690075344E-011 -7.189124056436E-003 # Dipole moment [bottom] (beta spin)
<rt_tddft>: 49.60000 -9.922042505097E-010 9.875665538895E-012 -4.762521613626E-003 # Dipole moment [bottom] (total spin)
<rt_tddft>: 49.60000 4.971528893584E-010 -1.059388025826E-010 2.616569755101E+000 # Dipole moment [top] (alpha spin)
<rt_tddft>: 49.60000 2.790925899946E-010 3.824681478124E-011 3.572964387441E+000 # Dipole moment [top] (beta spin)
<rt_tddft>: 49.60000 7.762456458594E-010 -6.769198780138E-011 -1.369369811779E+000 # Dipole moment [top] (total spin)
<rt_tddft>: 49.60000 -3.075350921188E-010 6.531697274133E-011 2.912826591179E+000 # Dipole moment [dimer] (alpha spin)
<rt_tddft>: 49.60000 2.873124185397E-010 -1.981039785684E-012 3.762160131710E+000 # Dipole moment [dimer] (beta spin)
<rt_tddft>: 49.60000 -2.022324950730E-011 6.333593295565E-011 -8.839172314311E-001 # Dipole moment [dimer] (total spin)


[3] rt_tddft_tcne_spinkick
The values of dipole moment of tests are close to the references. But they are not equal.
<< Reference >>
<rt_tddft>: 4.40000 5.378314947713E-005 -2.258995614124E-004 -1.036687663012E-004 # Dipole moment [system] (alpha spin)
<rt_tddft>: 4.40000 4.443994744641E-005 -2.419830623994E-004 -6.337834664515E-004 # Dipole moment [system] (beta spin)
<rt_tddft>: 4.40000 1.356207741932E-004 3.158870924835E-007 -1.069640539228E-004 # Dipole moment [system] (total spin)

<< Test result >>
<rt_tddft>: 4.40000 5.176872432699E-005 -2.258245188818E-004 -1.036657986595E-004 # Dipole moment [system] (alpha spin)
<rt_tddft>: 4.40000 4.283790373905E-005 -2.424890650128E-004 -6.337947649063E-004 # Dipole moment [system] (beta spin)
<rt_tddft>: 4.40000 1.320043054109E-004 -1.150729778132E-007 -1.069723847360E-004 # Dipole moment [system] (total spin)



<<< .bashrc >>>

  1. ~/.bashrc: executed by bash(1) for non-login shells.
  2. see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
  3. for examples

  1. If not running interactively, don't do anything
case $- in
   *i*) ;;
*) return;;
esac

  1. don't put duplicate lines or lines starting with space in the history.
  2. See bash(1) for more options
HISTCONTROL=ignoreboth

  1. append to the history file, don't overwrite it
shopt -s histappend

  1. for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000

  1. check the window size after each command and, if necessary,
  2. update the values of LINES and COLUMNS.
shopt -s checkwinsize

  1. If set, the pattern "**" used in a pathname expansion context will
  2. match all files and zero or more directories and subdirectories.
  3. shopt -s globstar

  1. make less more friendly for non-text input files, see lesspipe(1)
[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

  1. set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
   debian_chroot=$(cat /etc/debian_chroot)
fi

  1. set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
   xterm-color) color_prompt=yes;;
esac

  1. uncomment for a colored prompt, if the terminal has the capability; turned
  2. off by default to not distract the user: the focus in a terminal window
  3. should be on the output of commands, not on the prompt
  4. force_color_prompt=yes

if [ -n "$force_color_prompt" ]; then
   if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
# We have color support; assume it's compliant with Ecma-48
# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
# a case would tend to support setf rather than setaf.)
color_prompt=yes
   else
color_prompt=
   fi
fi

if [ "$color_prompt" = yes ]; then
   PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
   PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt

  1. If this is an xterm set the title to user@host:dir
case "$TERM" in
xterm*|rxvt*)
   PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
 ;;
  • )
   ;;
esac

  1. enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
   test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
alias ls='ls --color=auto'
#alias dir='dir --color=auto'
#alias vdir='vdir --color=auto'

   alias grep='grep --color=auto'
alias fgrep='fgrep --color=auto'
alias egrep='egrep --color=auto'
fi

  1. some more ls aliases
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'

  1. Add an "alert" alias for long running commands. Use like so:
  2. sleep 10; alert
alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\)"'

  1. Alias definitions.
  2. You may want to put all your additions into a separate file like
  3. ~/.bash_aliases, instead of adding them here directly.
  4. See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then
   . ~/.bash_aliases
fi

  1. enable programmable completion features (you don't need to enable
  2. this, if it's already enabled in /etc/bash.bashrc and /etc/profile
  3. sources /etc/bash.bashrc).
if ! shopt -oq posix; then
 if [ -f /usr/share/bash-completion/bash_completion ]; then
. /usr/share/bash-completion/bash_completion
elif [ -f /etc/bash_completion ]; then
. /etc/bash_completion
fi
fi
export PATH=$PATH:/home/user/octopus-4.1.2/octopus-4.1.2/bin

export USE_MPI=y
export BLASOPT="-lopenblas -lpthread -lrt"
export BLAS_SIZE=4
export USE_64TO32=y
export LARGE_FILES="TRUE"
export USE_NOFSCHECK="TRUE"
export LIB_DEFINES="-DDFLT_TOT_MEM=16777216"
export TCGRSH="usr/bin/ssh"
export NWCHEM_TOP="/home/user/NWChem-6.6/nwchem-6.6"
export NWCHEM_TARGET="LINUX64"
export NWCHEM_MODULES="all"
export PATH=$PATH:/home/user/NWChem-6.6/nwchem-6.6/bin

if [ -e /home/user/NWChem-6.6/Full_ECCE/ecce-builder-v7.0/scripts/runtime_setup.sh ]; then
      . /home/user/NWChem-6.6/Full_ECCE/ecce-builder-v7.0/scripts/runtime_setup.sh  
fi

    if [ -e /home/user/NWChem-6.6/ecce-builder/ecce-builder-v7.0/scripts/runtime_setup.sh ]; then
. /home/user/NWChem-6.6/ecce-builder/ecce-builder-v7.0/scripts/runtime_setup.sh
fi
  1. Add 2017-01-27
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.7
export PYTHONHOME=/usr

  • Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Threads 4
Posts 188
Hi Toshiharu,

You seem to have defined a simulation cell in your input above. The RT-TDDFT module is only available for finite or molecular systems. Just specify the coordinates within the geometry block.

Best,
-Niri
niri.govind@pnnl.gov

Clicked A Few Times
Threads 3
Posts 12
Dear Dr. Niri,
Thank you very much for your kind reply. I tried two kinds of tests. If you have any comment. Please teach me.
Best regards,

Toshiharu Higuchi
Yokohama, Japan

[1] Regarding the “Just specify the coordinates within the geometry block”, I deleted the NWPW block in the input above: H-GRH_SrcCode_170121A.nw. Then I tried the repeat tests under no make, no make link, and no change the above input file. However I got unreasonable results. Results are as follows.
Calculation results of Peak Field (V/cm)
(1) original =+7.48E7 (V/cm)
(2) 1st repetition= +1.61E7 / -7.25E7 (V/cm)
(3) 2nd repetition= +1.61E7 / -7.25E7 (V/cm)
(4) 3nd repetition= +6.05E7 / -3.26E7 (V/cm)

[2]Repeat test using NWChem text files under no make, no make link, and no change the input file.

[2-1] rt_tddft_dimer_charge in $NWCHEM_TOP/QA/tests.
I tried the four times repeat tests. As a result, I obtained the same value of dipole moment. It is a good result.

[2-2] Water TD-PBE0 resonant excitation: NWChem Documentation Release66, page 171
E-Field of 1st,2nd,and 3rd repetition have same value and these values correspond with the values of manual. However E-Field of original and 4th repetition did not correspond with the values of manual.
(1) Original = -3E-5 (a.u.)
(2) 1st repetition= +1E4 / -1E4 (a.u.)
(3) 2nd repetition= +1E4 / -1E4 (a.u.)
(4) 3rd repetition= +1E4 / -1E4 (a.u.)
(5) 4th repetition= +9.5E-5 (a.u.)


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