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				Problem in modifying the subroutine
			From NWChemViewed 519 times, With a total of 13 Posts 
            
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                            | Clicked A Few TimesThreads 3 Posts 12
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		                        | 1:23:05 PM PST - Tue, Jan 17th 2017 |  |  
		                        | 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)                          Warning: Dummy argument 'params' with INTENT(IN) in variable definition context (actual argument to INTENT = OUT/INOUT) at (1)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$
 
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                                     Edoapra  Forum:Admin, Forum:Mod, bureaucrat, sysop
                                    
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		                        | 11:55:48 AM PST - Thu, Jan 19th 2017 |  |  | sudo needed? 
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		                        | 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
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	| Edited On 11:57:00 AM PST - Thu, Jan 19th 2017 by Edoapra |  |  |  |  
            
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                            | Clicked A Few TimesThreads 3 Posts 12
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		                        | 5:20:35 AM PST - Fri, Jan 20th 2017 |  |  
		                        | 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
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                                     Edoapra  Forum:Admin, Forum:Mod, bureaucrat, sysop
                                    
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		                        | 1:59:26 AM PST - Sat, Jan 21st 2017 |  |  
		                        | 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)Warning: Dummy argument ‘params’ with INTENT(IN) in variable definition context (actual argument to INTENT = OUT/INOUT) at (1)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$
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                                     Edoapra  Forum:Admin, Forum:Mod, bureaucrat, sysop
                                    
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                            | Clicked A Few TimesThreads 3 Posts 12
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		                        | 6:22:41 PM PST - Tue, Jan 24th 2017 |  |  
		                        | 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
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                            | Clicked A Few TimesThreads 3 Posts 12
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		                        | 6:43:56 PM PST - Wed, Jan 25th 2017 |  |  
		                        | 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/cmWidth = 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[3] Step 3:Width = 1.26 fs
 
 
 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[4] Step 4:Width = 1.26 fs
 
 
 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/cmWidth = 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"
 
 
 NWPW define a simulation cell###
 
  SIMULATION_CELLENDcell_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
 
 
 
 geometry "system" units angstrom nocenter noautosym noautozgeometry###
 
    H     13.682904016    1.740899325    1.243493850    endC     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
 
 
 set geometry "system"
 
 basis
 
    H  library 3-21GendC  library 3-21G
 
 
 
 task dft###
 dft
 
 xc pbe0convergence energy 1e-5
 iterations 300
 vectors output H-GRH_SrcCode_170121A.movecs
 
 end
 
 
 task dft energy
 
 dplotdplot###
 
  TITLE HGRAendvectors 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
 
 
 task dft
 task dplot
 
 
 rt-tddft###
 unset rt_tddft:*
 rt_tddft
 
  tmax 400.0dt   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"
 
 
 Visualization###
 
  visualizationendtstart 0.0
 tend   400.0
 treference 0.0
 dplot
 end
 
 
 
 task dft rt_tddft
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                            | Gets AroundThreads 1 Posts 146
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		                        | 5:53:50 AM PST - Tue, Jan 31st 2017 |  |  
		                        | 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.
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                            | Clicked A Few TimesThreads 3 Posts 12
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		                        | 10:37:23 PM PST - Tue, Jan 31st 2017 |  |  
		                        | 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)
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                            | Gets AroundThreads 1 Posts 146
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		                        | 6:07:42 AM PST - Wed, Feb 1st 2017 |  |  
		                        | 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)? |  |  |  |  
            
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                            | Clicked A Few TimesThreads 3 Posts 12
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		                        | 11:54:26 PM PST - Wed, Feb 1st 2017 |  |  
		                        | 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 >>>
 
 
  ~/.bashrc: executed by bash(1) for non-login shells.
 see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
 for examples
 
 case $- in If not running interactively, don't do anything
 
    *i*) ;;esac*) return;;
 
 
 
 HISTCONTROL=ignoreboth don't put duplicate lines or lines starting with space in the history.
 See bash(1) for more options
 
 
 shopt -s histappend append to the history file, don't overwrite it
 
 
 HISTSIZE=1000 for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
 HISTFILESIZE=2000
 
 
 shopt -s checkwinsize check the window size after each command and, if necessary,
 update the values of LINES and COLUMNS.
 
 
  If set, the pattern "**" used in a pathname expansion context will
 match all files and zero or more directories and subdirectories.
shopt -s globstar
 
 [ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)" make less more friendly for non-text input files, see lesspipe(1)
 
 
 if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then set variable identifying the chroot you work in (used in the prompt below)
 
    debian_chroot=$(cat /etc/debian_chroot)fi
 
 
 case "$TERM" in set a fancy prompt (non-color, unless we know we "want" color)
 
    xterm-color) color_prompt=yes;;esac
 
 
  uncomment for a colored prompt, if the terminal has the capability; turned
 off by default to not distract the user: the focus in a terminal window
 should be on the output of commands, not on the prompt
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
 
    elsecolor_prompt=
    fifi
 
 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
 
 
 case "$TERM" in If this is an xterm set the title to user@host:dir
 xterm*|rxvt*)
 
    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1";;
 
   ;;esac
 
 
 if [ -x /usr/bin/dircolors ]; then enable color support of ls and also add handy aliases
 
    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'fialias fgrep='fgrep --color=auto'
 alias egrep='egrep --color=auto'
 
 
 
 alias ll='ls -alF' some more ls aliases
 alias la='ls -A'
 alias l='ls -CF'
 
 
 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$//'\)"' Add an "alert" alias for long running commands.  Use like so:
   sleep 10; alert
 
 
  Alias definitions.
 You may want to put all your additions into a separate file like
 ~/.bash_aliases, instead of adding them here directly.
 See /usr/share/doc/bash-doc/examples in the bash-doc package.
 if [ -f ~/.bash_aliases ]; then
 
    . ~/.bash_aliasesfi
 
 
 if ! shopt -oq posix; then enable programmable completion features (you don't need to enable
 this, if it's already enabled in /etc/bash.bashrc and /etc/profile
 sources /etc/bash.bashrc).
 
  if [ -f /usr/share/bash-completion/bash_completion ]; thenfi. /usr/share/bash-completion/bash_completion
 elif [ -f /etc/bash_completion ]; then
 . /etc/bash_completion
 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
 
 export USE_PYTHONCONFIG=y Add 2017-01-27
 export PYTHONVERSION=2.7
 export PYTHONHOME=/usr
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                            | 
                                  
                                     Niri  Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
                                    
                                   |  |  
                | 
                        
                            | Forum RegularThreads 4 Posts 190
 |  | 
		                    
		                        | 8:02:17 AM PST - Sat, Feb 11th 2017 |  |  
		                        | 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
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                | 
                        
                            | Clicked A Few TimesThreads 3 Posts 12
 |  | 
		                    
		                        | 9:29:58 PM PST - Sat, Feb 11th 2017 |  |  
		                        | 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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