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125 Commits

Author SHA1 Message Date
ccavazzoni 8a520cbe5d - adding support file for qmmm simulations to setup auxiliary quantities like 
atomic radii, which are not defined in the atomic code and makes the "fix"
  for LAMMPS more clumsy.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@12610 c92efa57-630b-4861-b058-cf58834340f0
 2016-07-25 07:22:56 +00:00
giannozz 02ce4df8d6 make.sys => make.inc. All other codes using make.sys should modify their build 
mechanism accordingly.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@12539 c92efa57-630b-4861-b058-cf58834340f0
 2016-06-25 07:26:50 +00:00
ccavazzoni fdf7766648 - FFT Modules replaced by FFTXlib 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@11857 c92efa57-630b-4861-b058-cf58834340f0
 2015-11-21 10:37:48 +00:00
giannozz bd6867cb1e Patch by Axel to ensure compilation on Windows 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@11840 c92efa57-630b-4861-b058-cf58834340f0
 2015-11-13 20:33:05 +00:00
giannozz d600cc5ea2 The string containing the MD5 hash could contain control character as it was 
not initialized in case of failure. Modified to return an error message


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@11780 c92efa57-630b-4861-b058-cf58834340f0
 2015-10-09 18:57:46 +00:00
giannozz 0c9876eea7 Preprocessing option __INTEL replaced by __INTEL_COMPILER that the compiler 
automatically recognizes. Please verify if clib/stack.c always compile or not.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@11761 c92efa57-630b-4861-b058-cf58834340f0
 2015-09-24 13:10:28 +00:00
paulatto 9982a6c061 Small change on previous commit: apparently (i.e. according to documentation) LoadLeveler send a SIGXCPU after soft_wall is reached and SIGKILL when har_wall is reached. I've added trapping of SIGXCPU. 
Wall clock limit is specified as:
  wall_clock_limit = 5:00,4:30
which would give pw 30 minutes to shut down





git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@11025 c92efa57-630b-4861-b058-cf58834340f0
 2014-06-04 14:23:19 +00:00
paulatto 63e85afa7f Added the possibility to intercept several signal and trigger a proper stop of the code, as if the file prefix.EXIT was found. 
Currently intercepted signals are SIGINT (caused by CTRL-C), SIGTERM (by default sent by PBS one minute before wall time expires), SIGUSR1, SIGUSR2

In order to compile this code add -D__TERMINATE_GRACEFULLY to MANUAL_DFLAGS in make.sys

This code partially conflicts with __TRAP_SIGUSR1, although they can both be compiled ony the last signal handler set will work. However they do the same thing, so __TRAP_SIGUSR1 could eventually be removed as it is less general. 

You can change the delay between the alert and the end of allocated wall time depending on the queue system. Here are some examples:

* with PBS:
  send the signal 120 seconds before the end:
  #PBS -l signal=@120

  send signal SIGUSR1 10 minutes before the end:
  #PBS -l signal=SIGUSR1@600

  you cand also send a signal manually with qsig, or send a signal and then stop:
   qdel -W 120 jobid
  will send SIGTERM, wait 2 minutes than force stop.

* with LodLeveler:
  According to documentation, a SIGUSR1 or a SIGTERM is sent, depending if the job will be restarted or not; SIGKILL follows after 2 minutes. There is no mention if this delay can be changed.



git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@11024 c92efa57-630b-4861-b058-cf58834340f0
 2014-06-04 14:12:13 +00:00
giannozz fd7d2618b1 Modified according to suggestion by Pizzi and Cepellotti 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10955 c92efa57-630b-4861-b058-cf58834340f0
 2014-05-09 19:04:20 +00:00
giannozz 7c01062ba0 Final (?) set of changes to the build system, especially for Windows (Axel) 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10590 c92efa57-630b-4861-b058-cf58834340f0
 2013-11-07 21:06:06 +00:00
giannozz d224f9d7b8 Small fixes for unitialized variables and questionable constructs, 
courtesy of Ake Sandgren


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10577 c92efa57-630b-4861-b058-cf58834340f0
 2013-11-05 14:35:41 +00:00
giannozz dab27f2c0d More cleanup of mpi modules, plus support for cross-compilation on windows 
using the mingw compiler (Axel)


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10573 c92efa57-630b-4861-b058-cf58834340f0
 2013-11-04 09:58:24 +00:00
giannozz 4338c04895 Fixes for more warnings (e.g. unitialized variables) by Axel 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10526 c92efa57-630b-4861-b058-cf58834340f0
 2013-10-10 14:24:18 +00:00
giannozz 41c8b628f1 Minor fixes by Axel to reduce the number of compiler warnings - harmless but 
too many of them may hide serious warnings


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10524 c92efa57-630b-4861-b058-cf58834340f0
 2013-10-10 12:46:35 +00:00
paulatto 4bccbf5dd8 l1 is an unsigned int: it cannot be negative, error is signaled by it being == 0 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10129 c92efa57-630b-4861-b058-cf58834340f0
 2013-04-09 13:44:09 +00:00
paulatto 99900e84ab Added a small C function to do a binary copy of a file and an interface to call it from fortran 
res = f_copy(source, dest)

returns:
 0 : no error
-1 : cannot open source
-2 : cannot open dest
-3 : error while writing
-4 : disk full while writing




git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10111 c92efa57-630b-4861-b058-cf58834340f0
 2013-04-07 15:34:07 +00:00
paulatto 3aff3512d1 avoid excessive complaining 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10053 c92efa57-630b-4861-b058-cf58834340f0
 2013-03-12 10:27:14 +00:00
paulatto 0db771c5c1 All c/fortran interfaces replace with iso_c_binding. 
f_mkdir replaced with a more explicit f_mkdir_safe, f_mkdir is now a direct wrapper of the POSIX function.

f_mkdir_safe now checks if a directory exists and is writable before creating it, it will only return error if at the end the directory is not writable
Possible causes: file exists but is not a directory; exists and is a directory, but not owned by the user; broken filesystem; perverted umask

check_tempdir does not change directly, but it benefits from the changes in f_mkdir_safe

parallel_mkdir replaced with check_tempdir where it was necessary



git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10052 c92efa57-630b-4861-b058-cf58834340f0
 2013-03-11 10:40:05 +00:00
giannozz e3358243f9 variable freed too earlyx 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10046 c92efa57-630b-4861-b058-cf58834340f0
 2013-03-10 19:33:55 +00:00
paulatto 785427abff Added double-check of tmp directory existing and being user-writable. This prevents unexpected crashes when outdir exists but is not a directory or is a directory owned by another user. 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10045 c92efa57-630b-4861-b058-cf58834340f0
 2013-03-10 13:44:28 +00:00
giannozz 6fd015975a Some cleanup of tmp_dir creation. It may break a few things, in particular the 
restart mechanism (it is already rather broken anyway). Notable changes:
- variable "restart" is set to true if restart_mode='restart' on input,
  independently upon the value of other variables
- the way tmp_dir and wfc_dir are created if not existent is simplified
- f_mkdir returns -1 if directory exists, 0 if created, 1 if error
- data-file.xml is no longer removed/renamed if restart_mode='from_scratch'. 
  I don't remember why it was done (although I remember there was a reason)
  and cannot see why it should be done. If restarting is dictated by input
  options, it shouldn't matter whether there is already a data-file.xml file
  on disk or not


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10031 c92efa57-630b-4861-b058-cf58834340f0
 2013-03-02 14:44:00 +00:00
giannozz f0e2f5a47c Minor corrections 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@10000 c92efa57-630b-4861-b058-cf58834340f0
 2013-02-21 08:26:04 +00:00
giannozz 6f7c3830d7 make.depend and scrpt generating them updated 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@9573 c92efa57-630b-4861-b058-cf58834340f0
 2012-10-24 14:31:17 +00:00
paulatto d70e0802d4 minor bugs 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@9542 c92efa57-630b-4861-b058-cf58834340f0
 2012-10-16 13:13:59 +00:00
paulatto 7350275bd6 fixed to not include any header if -D__PTRACE is not set 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@9511 c92efa57-630b-4861-b058-cf58834340f0
 2012-10-10 17:48:27 +00:00
paulatto 6754325b17 Added the possibility to do print backtrace symbols in case of error, 
compile with -D__PTRACE to activate.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@9508 c92efa57-630b-4861-b058-cf58834340f0
 2012-10-10 15:58:57 +00:00
paulatto e4e7d4e226 Apparently the t_mode c structure is not so trivial to use, removed the possobility to specify an umask in mkdir and removed the interface to chmod 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@8584 c92efa57-630b-4861-b058-cf58834340f0
 2012-02-06 15:03:21 +00:00
paulatto dd92bf644a Small fix because of mkdir returning -1 when directory already exists 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@8583 c92efa57-630b-4861-b058-cf58834340f0
 2012-02-06 14:50:38 +00:00
giannozz d54950b4e7 Harmless memory leak: missing deallocation 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@8216 c92efa57-630b-4861-b058-cf58834340f0
 2011-10-22 14:13:21 +00:00
giannozz b133da40d2 Added a few final deallocations - There should be no side effects, but 
I haven't tried all codes calling clean_pw (e.g. phonon)


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@8214 c92efa57-630b-4861-b058-cf58834340f0
 2011-10-21 21:22:04 +00:00
marsamos b077c491e5 forgot to clean patches before commit 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@7786 c92efa57-630b-4861-b058-cf58834340f0
 2011-05-17 09:39:46 +00:00
marsamos 051b652b95 deleted old GIPAW 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@7785 c92efa57-630b-4861-b058-cf58834340f0
 2011-05-17 09:38:53 +00:00
ccavazzoni 4e1dba6525 - adding symlink function to be used with PLUMED and CP 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@7698 c92efa57-630b-4861-b058-cf58834340f0
 2011-04-25 20:57:25 +00:00
marsamos 371ebb3859 add chdir to c_mkdir.c 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@7560 c92efa57-630b-4861-b058-cf58834340f0
 2011-03-10 16:40:29 +00:00
marsamos 352f0611e5 c_mkdir modified. Now returns value of -1 if he do not manage 
to create the dir and the dir does not exist, otherwise reurns value of 0.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@7443 c92efa57-630b-4861-b058-cf58834340f0
 2011-01-27 10:08:28 +00:00
degironc b91c455bb2 clean-up of the md5_from_file routine 
R.Sabatini (via SdG)


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@6995 c92efa57-630b-4861-b058-cf58834340f0
 2010-08-19 15:30:58 +00:00
giannozz 3e16cf2b10 New routine calculating md5 seems to work properly 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@6988 c92efa57-630b-4861-b058-cf58834340f0
 2010-08-18 14:39:50 +00:00
marsamos c673310ef8 io part of parallelization on images moved to image_io_routines. First step 
for NEB cleaning.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@6974 c92efa57-630b-4861-b058-cf58834340f0
 2010-08-17 15:39:53 +00:00
degironc b75413adf0 adding a few routines needed to calculate md5 checksum of a given file. 
They are intended to be used to calculate (and echo on the output) the
md5 checksum of the peudopotential files in order to be able to verify their
identity/integrity when comparing calculations performed at different
times or on different machines

R. Sabatini - S. de Gironcoli


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@6962 c92efa57-630b-4861-b058-cf58834340f0
 2010-08-13 10:50:08 +00:00
giannozz 4934b395ba Added signal processing by RdM. Disabled by default, enabled by option 
-D__TRAP_SIGUSR1 or using "./configure --enable-signals"


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@6370 c92efa57-630b-4861-b058-cf58834340f0
 2010-02-08 19:25:34 +00:00
giannozz 881fac18e1 Removed a few comments in C++ style (//). Some old compilers might complain. 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@6318 c92efa57-630b-4861-b058-cf58834340f0
 2010-01-26 14:06:59 +00:00
giannozz 04a06fec64 memstat.c modified to be compliant with C standard (picky compilers may complain) 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5998 c92efa57-630b-4861-b058-cf58834340f0
 2009-10-10 16:36:49 +00:00
giannozz 235929fb79 More of the same... 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5796 c92efa57-630b-4861-b058-cf58834340f0
 2009-08-01 20:55:14 +00:00
dalcorso 37fc952f13 ctrl+M removed. 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5544 c92efa57-630b-4861-b058-cf58834340f0
 2009-05-01 13:41:10 +00:00
kokalj 721f0716d5 Fixing an overflow bug: 
for(i=0;i-len-1;i++) strHelper[i]=' '

This was probably a typo and i<len-1 was meant.
This overflow bug had a very severe consequence on one of my
machine: all negative values were parsed as being positive.

Adding a check that a maximum size of len is 256, and also the length
of strHelper/strError strings changed to 257, or the last char in
strExpression was eaten. For more detailes see the file.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5517 c92efa57-630b-4861-b058-cf58834340f0
 2009-04-10 11:20:32 +00:00
ccavazzoni 8a2f375337 - char array (string) substituted with int array, name of function 
modified with the addition of _int suffix


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5503 c92efa57-630b-4861-b058-cf58834340f0
 2009-04-05 07:51:20 +00:00
ccavazzoni 98c33296cb - few more drivers useful in the MPI+OpenMP parallel FFT 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5488 c92efa57-630b-4861-b058-cf58834340f0
 2009-03-31 14:49:54 +00:00
giannozz 3675de688a #ifdef __INTEL moved inside clib/stack.c .The C code used to be compiled 
in all cases, causing problems in at least one obscure software configuration


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5482 c92efa57-630b-4861-b058-cf58834340f0
 2009-03-25 15:11:41 +00:00
giannozz 682e063081 Minor changes for Sun Sparcs 
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5263 c92efa57-630b-4861-b058-cf58834340f0
 2008-11-04 11:04:30 +00:00
giannozz 0b8cbf3b75 Configure modified so that it recognizes FFTW3 and FFT libraries from ACML. 
Mostly untested. Support for external fftw v.2 removed.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@5228 c92efa57-630b-4861-b058-cf58834340f0
 2008-10-18 14:40:51 +00:00