The established problem is the hashtable.f90 module; it throws errors I have tried to fix and cannot. At this time, my only answer is to use older binaries, statically linked. The 2016 versions at https://rsc.anu.edu.au/~username/ZMC.html seem to work on 64-bit, the older 2014 ones are 32-bit. This is my log of getting a working system.
First, this is a i386 install of Debian, so I downloaded the 2014 binaries from the RSC website:
https://rsc.anu.edu.au/~username/ZMC.html
ZMC and DZMC ran (created output file named 2021), but bin2gray did not, so I need to recompile, at least bin2gray. Bugger.
First, try naive approach — download and unpack the 2016 source files from the same website.
$ wget https://rsc.anu.edu.au/~username/ZMC_files/ZMC_toolbox_source_April_2016.tar.gz
Unpack it somewhere and …
$ sudo apt install gfortran
$ gfortran --version
GNU Fortran (Debian 8.3.0-6) 8.3.0
OK.
$ chmod +x compile_all_Linux_gfortran.sh
$ ./compile_all_Linux_gfortran.sh
OK, some of it compiled. Not bin2gray … but first let’s test the ZMC and DZMC binaries…
Nope, ZMC aborts. I bet it is the same hashtable.f90 issue I’ve had for years now.
OK. DZMC?
DZMC seems to work, although it puts some junk out to the command line when asking for the name of the diffuse.hkl file.
I don’t know if it is any faster than the precompiled binary, either. I guess we could test, but it feels slower.
OK, so now let’s look at bin2gray. Problem with reuse of variable names; change version to nversion:
$ diff bin2gray.f90 bin2gray-Linux-orig.f90
15c15
< character(len=*), parameter :: nversion = "$Id: bin2gray.f90,v 1.6 2007/06/04 05:23:11 aidan Exp $"
---
> character(len=*), parameter :: version = "$Id: bin2gray.f90,v 1.6 2007/06/04 05:23:11 aidan Exp $"
505c505
< write(myunit,*) nversion(6:index(version,":",back=.true.)-1)
---
> write(myunit,*) version(6:index(version,":",back=.true.)-1)
And now it compiles.
What about ZMC? It compiles but does not run properly; I cannot be bothered with that. Runtime errors, especially mysterious seg faults that move around when you add diagnostic output, are beyond my ken. As I recall a workaround is to avoid the use of keyword-based input file. I think I have a version somewhere that does this …
Install soft links to the binaries into ~/bin/ZMC and add that to my path.
$ ln -s /home/username/ZMC/source-2016/ZMC_toolbox_source_April_2016/bin2gray_static /home/username/bin/ZMC/bin2gray
and the rest from the 2014 source collection; for example:
$ cd ~/ZMC/RSC-2014/ZMCLinux/
$ for f in * ; do ln -s /home/username/ZMC/RSC-2014/ZMCLinux/$f /home/username/bin/ZMC/$f ; done
OK, that seems to be done.
-l ~/bin/ZMC/
total 4
lrwxrwxrwx 1 username username 76 Aug 17 19:28 bin2gray -> /home/username/ZMC/source-2016/ZMC_toolbox_source_April_2016/bin2gray_static
lrwxrwxrwx 1 username username 44 Aug 17 19:31 catmol2 -> /home/username/ZMC/RSC-2014/ZMCLinux/catmol2
lrwxrwxrwx 1 username username 44 Aug 17 19:31 chkmol2 -> /home/username/ZMC/RSC-2014/ZMCLinux/chkmol2
lrwxrwxrwx 1 username username 41 Aug 17 19:31 DZMC -> /home/username/ZMC/RSC-2014/ZMCLinux/DZMC
lrwxrwxrwx 1 username username 52 Aug 17 19:31 make_random_occ -> /home/username/ZMC/RSC-2014/ZMCLinux/make_random_occ
lrwxrwxrwx 1 username username 44 Aug 17 19:31 mol2xyz -> /home/username/ZMC/RSC-2014/ZMCLinux/mol2xyz
lrwxrwxrwx 1 username username 43 Aug 17 19:31 ni2pgm -> /home/username/ZMC/RSC-2014/ZMCLinux/ni2pgm
lrwxrwxrwx 1 username username 45 Aug 17 19:31 pgm2mask -> /home/username/ZMC/RSC-2014/ZMCLinux/pgm2mask
lrwxrwxrwx 1 username username 43 Aug 17 19:31 pgm2ni -> /home/username/ZMC/RSC-2014/ZMCLinux/pgm2ni
lrwxrwxrwx 1 username username 43 Aug 17 19:31 pgmave -> /home/username/ZMC/RSC-2014/ZMCLinux/pgmave
lrwxrwxrwx 1 username username 47 Aug 17 19:31 pgmcombine -> /home/username/ZMC/RSC-2014/ZMCLinux/pgmcombine
lrwxrwxrwx 1 username username 44 Aug 17 19:31 raw2pgm -> /home/username/ZMC/RSC-2014/ZMCLinux/raw2pgm
lrwxrwxrwx 1 username username 46 Aug 17 19:31 zmat2mol2 -> /home/username/ZMC/RSC-2014/ZMCLinux/zmat2mol2
lrwxrwxrwx 1 username username 45 Aug 17 19:31 zmat2xyz -> /home/username/ZMC/RSC-2014/ZMCLinux/zmat2xyz
lrwxrwxrwx 1 username username 46 Aug 17 19:31 zmat_anim -> /home/username/ZMC/RSC-2014/ZMCLinux/zmat_anim
lrwxrwxrwx 1 username username 44 Aug 17 19:31 zmatchk -> /home/username/ZMC/RSC-2014/ZMCLinux/zmatchk
lrwxrwxrwx 1 username username 47 Aug 17 19:31 zmat_maker -> /home/username/ZMC/RSC-2014/ZMCLinux/zmat_maker
lrwxrwxrwx 1 username username 40 Aug 17 19:31 ZMC -> /home/username/ZMC/RSC-2014/ZMCLinux/ZMC
So now let’s try bin2gray.
$ cd ~/ZMC/RSC-2014/ZMCLinux/Simple_Simn/
$ bin2gray --8bit 2021
File 2021 opened and irlen = 1600
---------------------------------------------------
---------------------------------------------------
The computation volume is defined by:
( -4.00, -4.50, 0.00) => ( 4.43, -4.50, 0.00)
( -4.00, -4.50, 0.00) => ( -4.43, 4.50, 0.00)
( -4.00, -4.50, 0.00) => ( -4.00, -4.50, 0.00)
Image size is 400 X 400 X 1
sin(theta)/lambda maximum = 0.686999977
Crystal size is: 32 32 32
Lot Size is: 9 9 6
Number of Lots Computed: 3
Subtract Average Lattice? e
Working on plane # 1/1 ...
Range = 4.84273769E-03 => 786.550415
Mean , STD = 15.257284623366822 38.963948929865644
Normalizing to 171.113083
Writing pgm 2021.pgm
$ sudo apt install imagej
$ imagej 2021.pgm
Needs JVM.
$ sudo apt install graphicsmagick netpbm
$ gm display 2021.pgm
OK, the image looks right. Maybe we’ll install ImageJ later or use it locally, because the JDK is so big.
In fact, just had to set JAVA_HOME:
$ which java
/usr/bin/java
For the session:
$ export JAVA_HOME=/usr
and then for future sessions:
$ echo "export JAVA_HOME=/usr" >> ~/.bashrc
OK, so we seem to have everything we might need to do some science.
We have:
* gfortran working
* ZMC and DZMC working (or at least the basic capabilities)
* bin2gray working
* the toolbox programs working (not all completely tested yet)
* imagej, netpbm and graphicsmagick all working.
OK for now.
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