setting up and running mac binary


  • Guest -
I am having trouble getting the binary set up and figuring out how to actually run nwchem on an input deck.
I downloaded/unarchived/uncompressed the binary for mac os 10.5/6. Not finding anything in the etc directory, I made a file per instructions given to another user elsewhere on this forum with the paths set for my system. Then I didn't know what to do with that file, so I just saved it as default.nwchemrc in etc.

Please bear with me as I have little experience on mac and even less with unix.

Thanks

Forum Vet
You may want to try nwchem myinputfile.nw , or simply running nwchem without an input file to see if it starts properly.

default.nwchemrc should be renamed as .nwchemrc .

Bert

Quote: Oct 17th 7:15 pm
I am having trouble getting the binary set up and figuring out how to actually run nwchem on an input deck.
I downloaded/unarchived/uncompressed the binary for mac os 10.5/6. Not finding anything in the etc directory, I made a file per instructions given to another user elsewhere on this forum with the paths set for my system. Then I didn't know what to do with that file, so I just saved it as default.nwchemrc in etc.

Please bear with me as I have little experience on mac and even less with unix.

Thanks

  • Guest -
I got nwchem to run an input deck as follows:
Quote:username
echo
title "total energy of benzene, B3LYP/3-21G"

start c6h6-b3lyp
scratch_dir /Users/wamsergroup/Desktop/scratch
permanent_dir /Users/wamsergroup/Desktop/perm

geometry
C    0.99261000     0.99261000     0.00000000
C -1.35593048 0.36332048 0.00000000
C 0.36332048 -1.35593048 0.00000000
C -0.99261000 -0.99261000 0.00000000
C 1.35593048 -0.36332048 0.00000000
C -0.36332048 1.35593048 0.00000000
H 1.75792000 1.75792000 0.00000000
H -2.40136338 0.64344338 0.00000000
H 0.64344338 -2.40136338 0.00000000
H -1.75792000 -1.75792000 0.00000000
H 2.40136338 -0.64344338 0.00000000
H -0.64344338 2.40136338 0.00000000
end

basis
  • library 3-21G
end

dft
 xc b3lyp
end

task dft energy

task dft optimize

task dft freq


The output looks good up until access of the basis libraries is attempted, at which point:
Quote:username
warning:::::::::::::: from_compile
 NWCHEM_BASIS_LIBRARY is: </Users/d3p852/Documents/nwchem-6.0/src/basis/libraries/>
but file does not exist or you do not have access to it !


Summary of "ao basis" -> "" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
* 3-21G on all atoms



                                NWChem DFT Module
-----------------


                      total energy of benzene, B3LYP/3-21G


Attempting to read a basis set from a  non-existing file:
/Users/d3p852/Documents/nwchem-6.0/src/basis/libraries/3-21g
------------------------------------------------------------------------
bas_tag_lib: failed opening basis file 0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
30: task dft energy
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error in the specified basis set
------------------------------------------------------------------------
[/quote]

Those paths are definitely not the ones on this machine, and the correct ones were set in the .nwchemrc file. I was thinking this might simply be because I have .nwchemrc in the wrong directory (Applications/nwchem-6.0-binary/etc rather than ./bin). But I'd thought I'd ask in case there might be some other reason.

  • Guest -
Generally .nwchemrc should be in your home directory (where your .bashrc and .cshrc are) as this is where it is going to look for them. Alternatively, you can also set an environment variable to point to the library: setenv NWCHEM_BASIS_LIBRARY <where you have the basis sets located> .

Bert

Quote: Oct 28th 7:35 pm
I got nwchem to run an input deck as follows:
Quote:username
echo
title "total energy of benzene, B3LYP/3-21G"

start c6h6-b3lyp
scratch_dir /Users/wamsergroup/Desktop/scratch
permanent_dir /Users/wamsergroup/Desktop/perm

geometry
C    0.99261000     0.99261000     0.00000000
C -1.35593048 0.36332048 0.00000000
C 0.36332048 -1.35593048 0.00000000
C -0.99261000 -0.99261000 0.00000000
C 1.35593048 -0.36332048 0.00000000
C -0.36332048 1.35593048 0.00000000
H 1.75792000 1.75792000 0.00000000
H -2.40136338 0.64344338 0.00000000
H 0.64344338 -2.40136338 0.00000000
H -1.75792000 -1.75792000 0.00000000
H 2.40136338 -0.64344338 0.00000000
H -0.64344338 2.40136338 0.00000000
end

basis
  • library 3-21G
end

dft
 xc b3lyp
end

task dft energy

task dft optimize

task dft freq


The output looks good up until access of the basis libraries is attempted, at which point:
Quote:username
warning:::::::::::::: from_compile
 NWCHEM_BASIS_LIBRARY is: </Users/d3p852/Documents/nwchem-6.0/src/basis/libraries/>
but file does not exist or you do not have access to it !


Summary of "ao basis" -> "" (cartesian)
------------------------------------------------------------------------------
Tag Description Shells Functions and Types
---------------- ------------------------------ ------ ---------------------
* 3-21G on all atoms



                                NWChem DFT Module
-----------------


                      total energy of benzene, B3LYP/3-21G


Attempting to read a basis set from a  non-existing file:
/Users/d3p852/Documents/nwchem-6.0/src/basis/libraries/3-21g
------------------------------------------------------------------------
bas_tag_lib: failed opening basis file 0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
30: task dft energy
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error in the specified basis set
------------------------------------------------------------------------
[/quote]

Those paths are definitely not the ones on this machine, and the correct ones were set in the .nwchemrc file. I was thinking this might simply be because I have .nwchemrc in the wrong directory (Applications/nwchem-6.0-binary/etc rather than ./bin). But I'd thought I'd ask in case there might be some other reason.

  • Guest -
Thanks for pointing me in the right general direction.
I don't know if this is universal to macs, but on mine setenv does not appear to be a recognized command when working from the bash terminal.
So, I made the environment variable according to instructions found here:
link Howto set shell-environment variables on Mac OSX 10.5
After doing this, everything is working fine for DFT.


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