We will take a look of your problem again.
Ray Luo, Ph.D.
On Jul 9, 2012, at 1:57 PM, Jan-Philip Gehrcke <jgehrcke.googlemail.com> wrote:
> Hey,
>
> this was kind of urgent to me, so I looked into the issue and resolved it. Attached you can find the fixed version of the amber12/AmberTools/src/pbsa/gen_dx_file.F90 as well as a patch file created via
>
> $ diff -u gen_dx_file.F90.orig gen_dx_file.F90 > gen_dx_file.F90.newline.patch
>
> As I've restructured the whole file en_dx_file.F90, the patch file is not really expressive. Things I've worked on:
>
> - fixed in subroutine `gen_dx_file`: if number of grid points is not an integer multiple of 3, the required newline character after the last data value is not written to DX output file.
>
> - fixed in subroutine `gen_dx_file`: DX output file name contains trailing spaces
>
> - cleaned up in subroutine `gen_dx_file`: variable names, variable declarations, code style
>
> - outcommented entire subroutines `printphidx` and `gen_integer_dx_file` in file gen_dx_file.F90 as they are not in use
>
> - rewrote file header, now including a link to DX format specification, the PBSA copyright header and author information
>
>
> I tested the new code and did not observe any problems.
>
>
> This is the first time I have worked with Fortran code. Ugh. I have comments/questions:
>
> 1) Shouldn't there be a central automatic 'newunit management' system in PBSA for preventing I/O collisions? Especially for large projects, the idea of relying on hard-coded numbers like `phifilenum=64` in pb_force.F90 seems to be risky. Are there plans for using the Fortran 2008 `newunit` feature, which automatically selects a unit number that does not interfere with other units in use?
>
> 2) In the Amber Fortran code style guidelines it is stated that people should not use the asterisk as format specifier. In gen_dx_file.F90, however, this is used quite heavily. I did not work on that, because all this Fortran formatting stuff seems to be pretty disgusting.
>
>
> I hope that course of action is fine with you.
>
> Cheers,
>
> Jan-Philip
>
>
>
> On 06/25/2012 07:44 PM, Ray Luo, Ph.D. wrote:
>> I'm forwarding this to Wes for a look ...
>>
>> Ray
>>
>> ---------- Forwarded message ----------
>> From: *Jan-Philip Gehrcke* <jgehrcke.googlemail.com
>> <mailto:jgehrcke.googlemail.com>>
>> Date: Mon, Jun 25, 2012 at 10:33 AM
>> Subject: [AMBER] AmberTools 12 pbsa: missing newline character in OpenDX
>> output
>> To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
>>
>>
>> Hello,
>>
>> there seems to be a small problem in the OpenDX-file-writing-feature of
>> pbsa in AmberTools 12. If the number of grid points is not an integer
>> multiple of 3, a missing newline character in the footer of the file
>> violates the format specification. These are the last few lines of a
>> problematic DX file written by pbsa:
>>
>> 1.3079431969E+01 1.2508119413E+01 1.1935395284E+01
>> 1.1363278074E+01 1.0795899087E+01 1.0246391314E+01
>> 9.7028066689E+00 9.1626945187E+00 8.6272002140E+00
>> 8.1016960668E+00 attribute "dep" string "positions"
>> object "Electrostatic Potential" class field
>> component "positions" value 1
>> component "connections" value 2
>> component "data" value 3
>>
>> There has to be a newline character before "attribute", according to
>> http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data
>>
>> VMD emits an error on attempting to load such a file. With the newline
>> character, VMD loads the file properly.
>>
>>
>> Regards,
>>
>> Jan-Philip Gehrcke
>>
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>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> <gen_dx_file.F90.newline.patch>
> <gen_dx_file.F90>
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Received on Mon Jul 09 2012 - 13:30:04 PDT
