From owner-nwchem-users@emsl.pnl.gov Wed Nov 1 13:21:27 2006 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id kA1LLQ8p022396 for ; Wed, 1 Nov 2006 13:21:27 -0800 (PST) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id kA1LLQ9V022395 for nwchem-users-outgoing-0915; Wed, 1 Nov 2006 13:21:26 -0800 (PST) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-IronPort-AV: i="4.09,379,1157353200"; d="scan'208"; a="10037073:sNHT42351680" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: [NWCHEM] RE: PSPW Problems Date: Wed, 1 Nov 2006 13:21:23 -0800 Message-ID: In-Reply-To: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: PSPW Problems Thread-Index: Acb8lHLcKQxTLs3LQxCU4WPYDv3qYgBZuWqA From: "Bylaska, Eric J" To: "Adrian Brown" Cc: X-OriginalArrivalTime: 01 Nov 2006 21:21:24.0626 (UTC) FILETIME=[AF4C2720:01C6FDFB] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by odyssey.emsl.pnl.gov id kA1LLPad022392 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Adrian, By using the program I just sent you I generated a new set of fractional coordinates which I used to generate the following input block. You should double check to make sure that I got things correct. I included an option in this input block which will generate a CIF file. Hope that helps Eric Bylaska title "Gypsum structure from Pedersen, B.F. and Semmingsen, D. Acta Crystalograp hica B38, 1074-1077 (1982)" start gypsum_optimize memory 500 mb #permanent_dir ./perm #scratch_dir ./perm geometry center noautoz noautosym units angstrom system crystal lat_a 5.679d0 lat_b 15.202d0 lat_c 6.522d0 alpha 90.0d0 beta 118.43d0 gamma 90.0d0 end Ca 0.500000 0.079670 0.250000 Ca 0.000000 0.579670 0.750000 Ca 0.000000 0.920330 0.250000 Ca 0.500000 0.420330 0.750000 S 0.000000 0.077050 0.750000 S 0.500000 0.577050 0.250000 S 0.500000 0.922950 0.750000 S 0.000000 0.422950 0.250000 O 0.963200 0.131900 0.550470 O 0.463200 0.631900 0.050470 O 0.036800 0.131900 0.949530 O 0.536800 0.631900 0.449530 O 0.463200 0.868100 0.550470 O 0.963200 0.368100 0.050470 O 0.536800 0.868100 0.949530 O 0.036800 0.368100 0.449530 O 0.758220 0.022260 0.667090 O 0.258220 0.522260 0.167090 O 0.241780 0.022260 0.832910 O 0.741780 0.522260 0.332910 O 0.258220 0.977740 0.667090 O 0.758220 0.477740 0.167090 O 0.741780 0.977740 0.832910 O 0.241780 0.477740 0.332910 O 0.379600 0.182120 0.458810 O 0.879600 0.682120 0.958810 O 0.620400 0.182120 0.041190 O 0.120400 0.682120 0.541190 O 0.879600 0.817880 0.458810 O 0.379600 0.317880 0.958810 O 0.120400 0.817880 0.041190 O 0.620400 0.317880 0.541190 H 0.251120 0.161580 0.503720 H 0.751120 0.661580 0.003720 H 0.748880 0.161580 0.996280 H 0.248880 0.661580 0.496280 H 0.751120 0.838420 0.503720 H 0.251120 0.338420 0.003720 H 0.248880 0.838420 0.996280 H 0.748880 0.338420 0.496280 H 0.404580 0.242750 0.492170 H 0.904580 0.742750 0.992170 H 0.595420 0.242750 0.007830 H 0.095420 0.742750 0.507830 H 0.904580 0.757250 0.492170 H 0.404580 0.257250 0.992170 H 0.095420 0.757250 0.007830 H 0.595420 0.257250 0.507830 end set nwpw:cif_filename gypsum nwpw mapping 2 energy_cutoff 5.0 loop 2 2 lmbfgs end set nwpw:lcao_skip .true. task pspw energy nwpw wavefunction_cutoff 36.0 energy_cutoff 36.0 ewald_ncut 8 ewald_rcut 3.0 end task pspw energy nwpw energy_cutoff 72.0 end task pspw energy task pspw optimize task pspw frequencies -----Original Message----- From: Adrian Brown [mailto:abrown@arc.nasa.gov] Sent: Monday, October 30, 2006 6:30 PM To: Bylaska, Eric J Subject: PSPW Problems Hi Eric, I am just using the PSPW module of NWChem to try and get vibrational frequencies for gypsum. I am struggling a bit with the right format for the simulation cell. Gypsum is a C2/c space group. I thought I had the right coordinates from a paper I have. This is what I am entering: ======================================= start gypsum_optimize title "Gypsum structure from Pedersen, B.F. and Semmingsen, D. Acta Crystalograp hica B38, 1074-1077 (1982)" geometry units angstrom system crystal lat_a 5.679d0 lat_b 15.202d0 lat_c 6.522d0 alpha 90.0d0 beta 118.43d0 gamma 90.0d0 end Ca .5 .07967 .25 S 0 .07705 .75 O1 .96320 .13190 .55047 O2 .75822 .02226 .66709 O3 .37960 .18212 .45881 H1 .25112 .16158 .50372 H2 .40458 .24275 .49217 end pspw simulation_cell units angstroms cell_name gypsum_c2/c boundary_conditions periodic end end set nwpw:minimizer 2 task pspw optimize task pspw frequencies ===================================================== Amongst all the outputs, I am getting the following errors: ... Memory information ------------------ heap = 39321601 doubles = 300.0 Mbytes stack = 13107201 doubles = 100.0 Mbytes global = 52428814 doubles = 400.0 Mbytes (within heap+stack) total = 52428802 doubles = 400.0 Mbytes ... rtdb_cget: array element is too small ... and then a bit later ... Error reading psi - bad grid Error reading psi - bad unitcell ... and then I have a memory problem ... - set nwpw:psi_nolattice .true. ------------------------------------------------------------------------ out of heap memory 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 53: task pspw optimize ------------------------------------------------------------------------ ------------------------------------------------------------------------ You need to assign at least 0 bytes more local memory ------------------------------------------------------------------------ For more information see the NWChem manual at http://www.emsl.pnl.gov/docs/nwchem/nwchem.html For further details see manual section: NWChem -> Top Level Directives -> Memory 0:0:out of heap memory:: 0 0:0:out of heap memory:: 0 Last System Error Message from Task 0:: Numerical result out of range 0: ARMCI aborting 0 (0). 0: ARMCI aborting 0 (0). system error message: Numerical result out of range Given that it seems to have 400Mb available, does it really need more memory? I was wondering if you can give me any hints as to what I have wrong - I think my coordinates are correct, but maybe you can spot another problem. Any hints would be greatly appreciated! Regards, Adrian -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Adrian Brown http://abrown.seti.org -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-