[Wien] setrlimit routine in Mac OS X platform
Hello, I'm trying to build the execution files on Mac OS X Lion platform with wien2k_12.1, gfortran, openblas, openmpi etc. then, I think that Mac OS X can't handle RLIM_INFINITY in setrlimit routine. so, I'd like to skip w2k_extend_limits() in W2kinit.F as below. *** ./SRC_hf/W2kinit.F.bak 2013-03-04 22:53:46.0 +0900 --- ./SRC_hf/W2kinit.F 2013-03-04 22:53:49.0 +0900 *** *** 27,33 --- 27,35 #ifdef INTEL_VML include 'mkl_vml.fi' #endif + #ifndef MACOSX call w2k_extend_limits() + #endif #ifdef Parallel ! Register C signal dispatcher, needed for parallel only *** ./SRC_lapw0/W2kinit.F.bak 2013-03-04 22:47:09.0 +0900 --- ./SRC_lapw0/W2kinit.F 2013-03-04 22:50:11.0 +0900 it seems to work well. but if there are any problems/precautions, please advise. Any information would be appreciated. With best regards, Tomo
[Wien] setrlimit routine in Mac OS X platform
Dear Laurence, thank you for your message. the gcc macro you pointed works well in my Mac OS X 10.7.4. please find the attached patch. Thanks again, with best regards, Tomo - Original Message - There should be W2kutils.c the lines #ifdef __APPLE__ limit.rlim_cur = limit.rlim_max ; /* RLIM_INFINITY */ #else limit.rlim_cur = RLIM_INFINITY ; #endif Maybe this is not being recognized in your Mac OS X, in which case try ( see http://lists.apple.com/archives/unix-porting/2004/Mar/msg00075.html ) adding #else ifdef __APPLE_CC__ limit.rlim_cur = limit.rlim_max ; /* RLIM_INFINITY */ and/or do what is suggested in the page above to see what is defined. Please let us know what works. On Tue, Mar 5, 2013 at 11:21 AM, tasaka at affinity-science.com tasaka at affinity-science.com wrote: Hello, I'm trying to build the execution files on Mac OS X Lion platform with wien2k_12.1, gfortran, openblas, openmpi etc. then, I think that Mac OS X can't handle RLIM_INFINITY in setrlimit routine. so, I'd like to skip w2k_extend_limits() in W2kinit.F as below. *** ./SRC_hf/W2kinit.F.bak 2013-03-04 22:53:46.0 +0900 --- ./SRC_hf/W2kinit.F 2013-03-04 22:53:49.0 +0900 *** *** 27,33 --- 27,35 #ifdef INTEL_VML include 'mkl_vml.fi' #endif + #ifndef MACOSX call w2k_extend_limits() + #endif #ifdef Parallel ! Register C signal dispatcher, needed for parallel only *** ./SRC_lapw0/W2kinit.F.bak 2013-03-04 22:47:09.0 +0900 --- ./SRC_lapw0/W2kinit.F 2013-03-04 22:50:11.0 +0900 it seems to work well. but if there are any problems/precautions, please advise. Any information would be appreciated. With best regards, Tomo ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- A non-text attachment was scrubbed... Name: apple.patch Type: text/x-patch Size: 4139 bytes Desc: not available URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130306/707ee2ca/attachment.patch
[Wien] Syntax error in array constructor (gfortran)
Dear Gavin, thank you for your reply. I agree and it might work well. but, I think it would be more favorable if source compatibility is kept in different compilers. Anyway, thanks again for your comments. With best regards, Tomo - Original Message - I think you have to modify the code like you indicated. I made the attached patch. It removed the compile time errors, but I never tested it make sure it didn't have any runtime errors. Placed gfortran.patch (for Wien2k 12.1) into $WIENROOT, and entered: $ patch -b -p0 -i gfortran.patch On 2/20/2013 11:26 PM, tasaka at affinity-science.com wrote: Hello, I encountered the follwoing errors when compiling in SRC_hf with GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3. if there are any options of gfortran to avoid these errors, please advise. // gfortran -ffree-form -O2 -ffree-line-length-none -c calc_exhfvv_tmp_.F calc_exhfvv_tmp_.F:269.22: igv = (/ 1:ng /) 1 Error: Syntax error in array constructor at (1) calc_exhfvv_tmp_.F:272.22: igv = (/ 1:(igs-1),(igs+1):ng /) 1 Error: Syntax error in array constructor at (1) make[1]: *** [calc_exhfvv.o] Error 1 // Or, should I modify the codes as like below? igv = (/ (i, i=1,ng,1) /) Any information would be appreciated. With best regards, Tomo ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Syntax error in array constructor (gfortran)
Hello, I encountered the follwoing errors when compiling in SRC_hf with GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3. if there are any options of gfortran to avoid these errors, please advise. // gfortran -ffree-form -O2 -ffree-line-length-none -c calc_exhfvv_tmp_.F calc_exhfvv_tmp_.F:269.22: igv = (/ 1:ng /) 1 Error: Syntax error in array constructor at (1) calc_exhfvv_tmp_.F:272.22: igv = (/ 1:(igs-1),(igs+1):ng /) 1 Error: Syntax error in array constructor at (1) make[1]: *** [calc_exhfvv.o] Error 1 // Or, should I modify the codes as like below? igv = (/ (i, i=1,ng,1) /) Any information would be appreciated. With best regards, Tomo
[Wien] trouble with clmcopy.def
Hello, I found that clmcopy can't work well in version 12.1. it's because of clmcopy.def. so, please modify/update x_lapw as below. tasaka at theta:~/work/tmp/SRC$ diff x_lapw x_lapw.new 1688,1689c1688,1689 echo 17,'$file.vresp$ending$updn', 'old','formatted', 0 echo 18,'$file.vresp$ending$dnup', 'unknown','formatted', 0 --- echo 17,'$file.vresp$ending$updn', 'old','formatted', 0$def echo 18,'$file.vresp$ending$dnup', 'unknown','formatted', 0$def 1691,1692c1691,1692 echo 17,'$file.clm$ending$updn', 'old','formatted', 0 echo 18,'$file.clm$ending$dnup', 'unknown','formatted', 0 --- echo 17,'$file.clm$ending$updn', 'old','formatted', 0$def echo 18,'$file.clm$ending$dnup', 'unknown','formatted', 0$def tasaka at theta:~/work/tmp/SRC$ With best regards, Tomo
[Wien] job submission script for grid engine
Hello,
I wrote a simple script to submit wien2k's parallel job into grid
engine queueing system. I suppose it works without errors,
but I don't have a sufficient testing environment now(only single node).
so, I would appreciate if anyone could check the following and fix if it
's wrong.
Thanks in advance, with best regards,
Tomo
#!/bin/csh
#$ -S /bin/csh
#$ -N WIEN2k_JOB
#$ -cwd
#$ -q all.q
#$ -V
#$ -j y
#$ -o sge.out
#$ -pe mpi 16
set core = 4
set kdiv = 4
@ node_per_k = ${NSLOTS} / ${core} / ${kdiv}
#date
echo NSLOTS: $NSLOTS
echo kdiv x node_per_k, core: $kdiv x $node_per_k, $core
#cat $PE_HOSTFILE
#uniq -c $PE_HOSTFILE
#/bin/echo -e $NSLOTS
if ( -e .machines ) then
#cp .machines .machines_old
rm .machines
endif
echo -n 'lapw0: ' .machines
cat $PE_HOSTFILE | awk '{printf $1:$2 }' .machines
echo .machines
cat $PE_HOSTFILE | awk '{if('${core}' $2) \
{ print Check $core or alloc.rule!} \
i=1 \
while(i = $2/'${core}' ) \
{ printf $1:'${core}'\n \
i++ } \
}' .machines_tmp_$$
cat .machines_tmp_$$ | awk '{if(NR%'${node_per_k}') ORS= \
else ORS=\n; print}' | sed -e 's/^/1\:/g' .machines
rm .machines_tmp_$$
echo 'granularity:1' .machines
echo 'extrafine:1' .machines
# write down wien2k-job
#init_lapw -red 2 -vxc 13 -rkmax 6.5 -numk 200 -b
#testpara
#run_lapw -I -i 40 -p
#x_lapw lapw1 -up -p
#x_lapw qtl -up -p
[Wien] way to confirm stable/transition structures
Hi, thank you for the detailed explanations. this is always the case which are well known although often omitted in simple textbooks. I am 99.8% certain that MSR1a will also not be trapped in a saddle point although there is currently no analytic proof of this. I agreed, it was a help to me! With best regards, Tomo - Original Message - This is a slightly complicated question. What you sent is a transition state, mathematically a saddle point. You are asking if within MINI (and/or MSR1a) you can get trapped in one. I can only answer for PORT MSR1a. If you start a little away from a saddle point, and there are no other issues such as problems with touching RMTs or inconsistent forces, the program will converge to a true local minimum. There are some standard traps that ensure that this is always the case which are well known although often omitted in simple textbooks. I am 99.8% certain that MSR1a will also not be trapped in a saddle point although there is currently no analytic proof of this. A caveat. If you were to start at the exact saddle point (or very close to it) the mini code may decide that you have already converged and stop without checking. This is because the convergence criteria are just that the forces are small, not that the Hessian is positive definite (i.e. a local minimum). Another caveat. If you have a soft mode distortion away from the saddle point the code might also be fooled into thinking it has found a minimum whereas in reality it has not. PORT is quite good in avoiding this; MSR1a not quite so good for a number of reasons. And yet a third one. It is possible to force a saddle point using symmetry, for instance if you added a z-axis mirror. If you are concerned whether you have got trapped in a saddle point because you started there, move the atomic positions a bit and rerun. N.B., a different question is how to find a saddle point/transition state. On Fri, Oct 5, 2012 at 4:55 AM, tasaka at affinity-science.com tasaka at affinity-science.com wrote: Hello, In MINI calculation, a relaxed structure is depend on initial structure in general. so, sometimes it might arrive to the transition structure. for example, please find the attached structure file. for that case, how do we confirm the obtained structure whether transition or stable structure, especially in wien2k-code? sorry if it's a silly question, but any information would be appreciated. With best regards, Tomo -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] way to confirm stable/transition structures
Hello, In MINI calculation, a relaxed structure is depend on initial structure in general. so, sometimes it might arrive to the transition structure. for example, please find the attached structure file. for that case, how do we confirm the obtained structure whether transition or stable structure, especially in wien2k-code? sorry if it's a silly question, but any information would be appreciated. With best regards, Tomo -- next part -- A non-text attachment was scrubbed... Name: ethane.struct Type: application/octet-stream Size: 2316 bytes Desc: not available URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20121005/902fb62e/attachment.dll
