From owner-nwchem-users@emsl.pnl.gov Sun Jun 15 17:28:01 2008 Received: from odyssey.emsl.pnl.gov (localhost.pnl.gov [127.0.0.1]) by odyssey.emsl.pnl.gov (8.14.1/8.14.1) with ESMTP id m5G0S00R024782 for ; Sun, 15 Jun 2008 17:28:01 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id m5G0S0NG024781 for nwchem-users-outgoing-0915; Sun, 15 Jun 2008 17:28:00 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-IronPort-AV: E=Sophos;i="4.27,649,1204531200"; d="scan'208";a="78015644" 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" Content-Transfer-Encoding: quoted-printable Subject: RE: [NWCHEM] GUI for plane wave? Date: Sun, 15 Jun 2008 17:27:58 -0700 Message-ID: In-Reply-To: <728224.46625.qm@web54405.mail.yahoo.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] GUI for plane wave? Thread-Index: AcjPJaf9UHGEmVRFSx26yLDH8q7/aAAIVzWg References: <728224.46625.qm@web54405.mail.yahoo.com> From: "Bylaska, Eric J" To: , X-OriginalArrivalTime: 16 Jun 2008 00:27:58.0663 (UTC) FILETIME=[D402A570:01C8CF47] Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Here's a simple input deck that uses the steepest descent code to generate an initial solvent configuration around a niobate cluster. =20 Note in this input a couple of the MM water molecules are on top of each other. ################################################################# title "Nb10O28^{-6} + water112 - 374 atom cell" start decaniobate-water112 memory 1500 mb permanent_dir /scratch/scratchdirs/ebylaska/Decaniobate-QMMM/perm scratch_dir /scratch/scratchdirs/ebylaska/Decaniobate-QMMM/perm charge -6 geometry units angstrom nocenter noautosym noautoz print xyz Nb -7.57935 12.39392 5.82331 Nb -1.25825 10.34502 2.62740 Nb -7.35842 12.74471 2.47472 Nb -1.47918 9.99423 5.97600 Nb -4.52852 11.18604 5.95178 Nb -4.30908 11.55290 2.49894 Nb -6.83072 9.73261 3.88253 Nb -2.00687 13.00633 4.56818 Nb -5.07546 14.19719 4.47987 Nb -3.76214 8.54175 3.97085 O -8.79615 12.73973 7.01530 O -0.04145 9.99921 1.43542 O -5.62596 12.21449 1.42328 O -3.21164 10.52444 7.02744 O -4.44407 15.82760 4.69982 O -4.39353 6.91134 3.75089 O -7.47420 8.13582 3.62397 O -1.36340 14.60312 4.82675 O -3.62843 13.32110 3.21863 O -5.20916 9.41784 5.23208 O -3.79184 13.04921 5.71812 O -5.04576 9.68973 2.73260 O -8.39267 12.93400 4.12206 O -0.44492 9.80494 4.32865 O -8.45200 13.30412 1.22915 O -0.38560 9.43482 7.22157 O -6.46525 14.04965 5.78035 O -2.37235 8.68929 2.67036 O -6.27779 14.32665 2.99329 O -2.55981 8.41229 5.45743 O -7.84671 10.49633 5.31803 O -0.99089 12.24261 3.13269 O -7.66277 10.78340 2.51069 O -1.17482 11.95554 5.94003 O -6.00398 11.62476 6.95321 O -2.83361 11.11417 1.49751 O -5.70017 11.88912 4.18132 O -3.13743 10.84982 4.26939 O^ -6.68146 9.29108 0.93789 H^ -7.32146 8.58008 0.96389 H^ -6.31946 9.26608 0.05189 O^ -4.82346 11.34708 -1.32411 H^ -4.53246 11.37308 -2.23611 H^ -5.30046 10.52108 -1.24011 O^ -5.49046 14.91308 -0.65411 H^ -6.29746 15.08208 -0.16811 H^ -5.18546 15.77508 -0.93511 O^ -5.67246 10.18908 9.44989 H^ -6.42846 10.72908 9.21789 H^ -5.99646 9.58208 10.11489 O^ -6.63746 16.68708 5.44689 H^ -7.50246 16.49808 5.08189 H^ -6.77246 17.43608 6.02689 O^ -2.99346 13.09708 9.26389 H^ -2.35446 12.47108 8.92289 H^ -3.74346 12.56508 9.53089 O^ -10.60246 9.60408 5.38089 H^ -10.40846 8.71208 5.09389 H^ -10.93146 9.51008 6.27489 O^ -3.79646 7.61808 -0.24811 H^ -3.94046 7.72208 0.69289 H^ -2.87546 7.83908 -0.38411 O^ -2.30846 16.68708 0.88589 H^ -1.80746 16.05308 0.37189 H^ -2.20846 16.40308 1.79489 O^ -7.03346 6.04508 1.54789 H^ -6.88046 6.24508 2.47089 H^ -7.96246 5.82208 1.49389 O^ -9.80046 8.44108 1.75589 H^ -9.01246 7.92808 1.93589 H^ -10.52646 7.88908 2.04589 O^ 1.65054 13.17308 4.87689 H^ 0.86354 13.71608 4.91989 H^ 1.34154 12.31108 4.59789 O^ -5.75246 5.34808 5.33089 H^ -6.33746 4.96208 5.98189 H^ -5.30646 6.06008 5.78989 O^ 0.52454 14.21408 1.04389 H^ -0.01946 14.99908 0.98289 H^ 1.42454 14.53908 1.08189 O^ -8.02746 7.54708 7.72489 H^ -7.41246 7.75708 7.02089 H^ -7.73946 6.69708 8.05889 O^ -0.65446 15.62808 7.02789 H^ -0.45246 15.50208 7.95489 H^ -0.03646 15.06608 6.56089 O^ -11.23146 13.02008 1.85889 H^ -10.98346 13.68208 1.21389 H^ -11.24346 13.48308 2.69689 O^ -7.07546 17.95308 2.28489 H^ -6.19246 17.77208 2.60689 H^ -6.95146 18.53408 1.53489 O^ -2.85746 13.82108 -2.60711 H^ -2.16846 13.17008 -2.74311 H^ -3.59046 13.52208 -3.14511 O^ -2.34146 5.02208 2.57689 H^ -3.13046 5.54408 2.43289 H^ -1.90246 5.43708 3.31989 O^ -9.25746 16.00608 7.39289 H^ -9.53146 15.14908 7.06689 H^ -8.32246 16.05908 7.19489 O^ -4.63346 16.17308 9.24989 H^ -5.53246 16.25308 8.93089 H^ -4.11246 16.72008 8.66289 O^ -3.97346 7.17408 9.55789 H^ -3.67146 6.79008 10.38089 H^ -4.88646 6.89908 9.47789 O^ -10.22846 16.35408 4.29689 H^ -10.31046 15.71908 5.00889 H^ -11.05946 16.30408 3.82389 O^ -7.41046 9.36808 -2.26811 H^ -6.68846 9.99008 -2.35611 H^ -6.99646 8.50408 -2.28911 O^ -2.64846 9.41608 -2.88211 H^ -2.58246 8.70908 -2.24111 H^ -1.77346 9.48908 -3.26211 O^ -5.00746 18.19808 -0.29411 H^ -5.49846 19.01008 -0.41511 H^ -4.10446 18.41708 -0.52511 O^ 2.33354 11.74708 -0.26411 H^ 2.88454 12.52408 -0.16911 H^ 1.73354 11.77708 0.48089 O^ 0.30854 13.37608 -2.21411 H^ 0.75754 13.78308 -1.47311 H^ 0.01554 14.10708 -2.75811 O^ 0.20154 7.37808 7.95789 H^ -0.59146 7.81108 8.27589 H^ 0.43554 6.75408 8.64489 O^ -8.81646 15.13108 -1.05411 H^ -8.52946 15.56208 -1.86011 H^ -8.01446 14.79208 -0.65611 O^ 0.98454 6.63208 4.37289 H^ 1.20954 6.11908 5.14789 H^ 0.13954 7.03208 4.57689 O^ 0.80354 11.11408 8.56289 H^ -0.10046 11.13508 8.87689 H^ 1.18854 10.33808 8.96889 O^ -5.79646 13.18308 11.10989 H^ -6.34646 13.95908 11.00689 H^ -5.78046 12.77408 10.24489 O^ 1.85054 16.25008 3.46289 H^ 1.63854 15.87808 4.31889 H^ 1.94554 17.18908 3.61689 O^ -0.42746 18.55008 2.88589 H^ -0.56546 19.37508 2.41989 H^ -0.83446 18.67808 3.74189 O^ -7.09146 12.97908 -3.01211 H^ -7.43246 13.64608 -2.41611 H^ -6.45146 13.43808 -3.55611 O^ -10.42146 6.22308 5.61789 H^ -9.62846 6.38808 5.10889 H^ -10.27146 6.65608 6.45889 O^ -10.73046 9.18808 8.65389 H^ -11.30746 8.71408 9.25389 H^ -10.10346 9.63908 9.21889 O^ -6.44546 6.24708 -1.72011 H^ -6.87446 6.52008 -0.90811 H^ -6.52146 5.29308 -1.73111 O^ 0.12454 14.10108 9.87189 H^ 0.68454 13.46108 9.43289 H^ -0.76046 13.91008 9.56089 O^ -10.70046 9.46908 -1.26611 H^ -10.83846 10.39308 -1.47611 H^ -11.56346 9.06408 -1.35211 O^ -2.89646 10.40208 11.26689 H^ -3.38446 9.70708 11.70889 H^ -1.98746 10.28008 11.54289 O^ -2.56446 18.25508 7.73789 H^ -1.61246 18.26708 7.63789 H^ -2.71646 18.39508 8.67189 O^ -0.80046 16.47408 -1.99111 H^ -1.26646 15.65508 -2.15911 H^ -1.41546 17.01108 -1.49011 O^ 0.89154 7.85508 -0.45311 H^ 1.37154 7.06508 -0.20611 H^ 0.47354 7.64008 -1.28711 O^ -8.51546 4.21408 3.84389 H^ -7.78946 3.59308 3.89889 H^ -9.26246 3.75808 4.23089 O^ -4.51846 4.31608 0.21189 H^ -3.77846 3.76508 0.46589 H^ -4.57546 4.23208 -0.74011 O^ -3.53446 4.46008 7.67289 H^ -3.26346 3.54208 7.66789 H^ -4.34546 4.48208 7.16589 O^ -8.41346 15.21808 10.55389 H^ -9.22946 15.19108 10.05489 H^ -8.45046 16.03808 11.04689 O^ -1.36246 5.42708 -0.57511 H^ -1.00546 5.69608 -1.42111 H^ -2.29546 5.28708 -0.73311 O^ -8.33246 18.40208 -0.78711 H^ -8.34046 18.74008 0.10789 H^ -7.77546 17.62408 -0.75311 O^ -10.76446 16.82308 1.04589 H^ -11.20646 17.57108 0.64589 H^ -11.11246 16.77708 1.93689 O^ -4.07646 16.82308 -3.13411 H^ -4.73046 16.14208 -2.97311 H^ -3.25246 16.35108 -3.25711 O^ -7.04746 18.23308 8.43589 H^ -6.17446 18.61608 8.35289 H^ -6.90646 17.38208 8.85089 O^ -10.25246 5.21808 1.12289 H^ -9.75946 6.02608 0.97789 H^ -10.86946 5.17008 0.39189 O^ -11.45946 12.97608 -1.52711 H^ -11.81646 12.93908 -0.63911 H^ -10.51146 13.03708 -1.41011 O^ 1.09054 5.10608 1.52589 H^ 1.26754 4.54008 2.27789 H^ 1.49054 4.66008 0.77989 O^ -7.08846 7.57108 10.92389 H^ -6.93446 7.32208 11.83489 H^ -7.97346 7.26408 10.72889 O^ -6.54646 4.90308 8.81789 H^ -7.07646 4.71008 8.04389 H^ -6.15746 5.76008 8.64489 O^ -12.44246 6.82208 3.09789 H^ -11.91346 6.04408 3.27589 H^ -12.52646 6.85208 2.14489 O^ 0.22354 11.37908 11.84889 H^ -0.71746 11.35208 12.02389 H^ 0.30554 11.20408 10.91189 O^ -0.69146 3.72608 5.21689 H^ -0.05646 3.05908 4.95789 H^ -0.89746 4.19908 4.41089 O^ -8.17246 10.71808 11.56189 H^ -9.01946 10.65508 12.00289 H^ -7.59846 10.12208 12.04289 O^ -8.90446 19.07908 5.66289 H^ -9.29546 19.66908 6.30689 H^ -8.76446 18.25708 6.13289 O^ 3.64154 13.18608 2.35489 H^ 2.78054 12.96208 2.70989 H^ 3.52454 13.18808 1.40489 O^ 2.72654 13.84708 7.86389 H^ 2.76254 14.60908 7.28589 H^ 2.91454 13.09708 7.29889 O^ 0.42354 18.52808 6.02889 H^ 1.17254 17.94108 5.92589 H^ -0.33146 18.02108 5.72989 O^ -1.64946 16.73808 10.53589 H^ -1.35646 17.35308 9.86389 H^ -2.52846 16.47508 10.26289 O^ -3.43946 5.70408 -3.04611 H^ -3.81946 6.47608 -2.62811 H^ -2.51846 5.70908 -2.78611 O^ -12.25146 14.92308 7.88689 H^ -11.46546 14.85608 7.34489 H^ -12.08046 15.65408 8.48089 O^ -0.93146 7.86708 11.00489 H^ -1.42346 8.64808 11.25889 H^ -0.79046 7.38708 11.82089 O^ -8.95646 3.61008 7.05289 H^ -9.80946 3.85908 7.40889 H^ -8.32546 4.16308 7.51489 O^ -9.88146 19.65008 2.50689 H^ -10.24646 19.63208 3.39189 H^ -10.18846 18.84308 2.09489 O^ -9.66746 6.46908 -1.89911 H^ -9.10146 7.21908 -1.71411 H^ -9.16646 5.92508 -2.50611 O^ 1.34054 17.35608 0.34389 H^ 1.36754 16.88608 -0.49011 H^ 0.51854 17.84608 0.32589 O^ 1.08154 10.05308 -2.96811 H^ 1.59754 9.33408 -2.60611 H^ 0.95454 10.66008 -2.23911 O^ -1.03046 4.81508 9.73089 H^ -0.33246 5.47008 9.69489 H^ -0.72346 4.09508 9.17989 O^ -0.39146 7.04108 -3.42411 H^ -0.13946 6.32408 -4.00711 H^ -0.23846 6.70608 -2.54111 O^ 4.05654 10.70208 8.30389 H^ 3.49654 10.38608 7.59489 H^ 3.61554 10.43008 9.10889 O^ 3.19854 7.82908 6.76289 H^ 3.34954 8.30208 7.58189 H^ 2.59654 8.38208 6.26489 O^ 3.17054 16.74308 6.44689 H^ 3.89754 16.94308 5.85689 H^ 3.57454 16.62708 7.30689 O^ 3.18554 14.87408 -0.85711 H^ 2.82754 15.34208 -1.61111 H^ 3.25954 13.96308 -1.14411 O^ 1.34054 17.19208 9.15289 H^ 1.55554 17.59808 8.31289 H^ 0.90454 17.88008 9.65589 O^ -11.71746 11.17108 11.18189 H^ -11.77746 11.40208 12.10889 H^ -11.71046 12.00908 10.71889 O^ -10.44146 5.84008 9.10289 H^ -10.10446 6.65008 8.71989 H^ -10.57446 6.03908 10.02889 O^ -1.27046 19.48008 -0.45611 H^ -1.86046 18.96408 0.09289 H^ -1.80646 19.76508 -1.19611 O^ -11.54746 16.47308 -2.22811 H^ -10.81146 16.83608 -2.72111 H^ -11.22746 15.64108 -1.88111 O^ -10.29546 8.06808 11.73589 H^ -9.92346 8.88208 11.39589 H^ -9.91646 7.37708 11.19389 O^ -12.10746 17.94808 6.39589 H^ -12.66646 18.07508 5.62989 H^ -11.69446 17.09508 6.26289 O^ 2.24354 8.67008 10.26789 H^ 3.08854 9.09108 10.42989 H^ 2.05554 8.17808 11.06789 O^ 1.88254 4.70608 7.09489 H^ 2.67754 5.16608 7.36389 H^ 1.30254 4.74708 7.85589 O^ -10.66946 17.83608 9.62789 H^ -10.45146 17.54008 8.74489 H^ -11.49946 18.30508 9.53389 O^ -4.15046 4.38608 11.19889 H^ -3.20646 4.44908 11.05089 H^ -4.53046 5.09508 10.67989 O^ -4.23246 19.04908 10.71489 H^ -4.57146 18.18908 10.96289 H^ -4.04746 18.98308 9.77889 O^ 3.09654 12.56508 10.87989 H^ 2.74654 12.80708 10.02189 H^ 2.95854 13.33608 11.42989 O^ -5.90946 3.10808 -2.55811 H^ -5.65646 3.77308 -1.91711 H^ -6.82246 2.90308 -2.35511 O^ 1.96354 15.91208 -3.77011 H^ 2.33054 15.10408 -4.12811 H^ 1.43854 15.63408 -3.02011 O^ -7.33646 18.10508 11.72989 H^ -6.83046 17.78208 12.47489 H^ -6.83246 18.84408 11.38889 O^ -11.52246 14.49608 11.07389 H^ -11.57746 15.28908 10.53989 H^ -10.60946 14.21808 11.01189 O^ 2.98954 7.24308 -2.95611 H^ 3.30454 8.06808 -2.58711 H^ 2.52954 7.49008 -3.75811 O^ 1.58054 4.56608 -1.72611 H^ 2.38954 5.06608 -1.83511 H^ 0.88454 5.22308 -1.70411 O^ 2.76954 19.34908 3.70289 H^ 3.36154 19.79508 4.30889 H^ 1.93254 19.30208 4.16389 O^ 3.38154 4.31508 4.13889 H^ 2.45254 4.53108 4.22589 H^ 3.56454 3.71308 4.85989 O^ -11.75646 3.63508 3.98489 H^ -11.13846 3.52608 3.26189 H^ -12.05946 4.54008 3.91689 O^ -8.49046 4.65108 11.54789 H^ -9.43446 4.62808 11.70189 H^ -8.12546 5.09908 12.31089 O^ -9.20546 3.29808 -2.43911 H^ -9.79446 3.01308 -1.74011 H^ -9.63146 3.02408 -3.25011 O^ 3.24554 12.66308 -3.47011 H^ 4.06454 12.45808 -3.01911 H^ 2.59954 12.77208 -2.77311 O^ 1.33254 19.01508 -2.56811 H^ 0.85354 19.64708 -3.10511 H^ 0.68254 18.66408 -1.95911 O^ 2.13454 5.40708 10.31489 H^ 2.11354 5.87808 11.14789 H^ 2.91654 4.85808 10.35989 O^ -9.75046 18.68908 -3.83611 H^ -9.29346 19.51208 -4.00811 H^ -9.07146 18.01508 -3.87911 O^ -12.25946 4.35008 -1.86311 H^ -12.82946 4.94008 -2.35711 H^ -12.60146 3.47308 -2.03711 end set nwpw:cif_filename decaniobate #set qmmm=20 NWPW QMMM lj_ion_parameters Nb 3.16555789d0 0.15539425d0 lj_ion_parameters O 3.16555789d0 0.15539425d0 lj_ion_parameters O^ 3.16555789d0 0.15539425d0 # new input format fragment spc size 3 index_start 39:372:3 shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0 #bond_spring 1 2 0.467307856 1.889726878 #bond_spring 1 3 0.467307856 1.889726878 #angle_spring 2 1 3 0.07293966 1.910611932 end END END #***** Setup and run conjugate gradient code **** nwpw SIMULATION_CELL SC 30.0 END mapping 2 cutoff 1.0 lmbfgs ewald_ncut 1 end set nwpw:lcao_skip .true. task pspw gradient set geometry:actlist 39:374 nwpw steepest_descent geometry_optimize time_step 1.0d-8 loop 10 20 ewald_ncut 1 end end task pspw steepest_descent nwpw; steepest_descent; time_step 1.0e-7; end; end; task pspw steepest_descent nwpw; steepest_descent; time_step 1.0e-6; end; end; task pspw steepest_descent nwpw; steepest_descent; time_step 1.0e-5; end; end; task pspw steepest_descent nwpw; steepest_descent; time_step 1.0e-4; end; end; task pspw steepest_descent nwpw; steepest_descent; time_step 1.0e-3; end; end; task pspw steepest_descent nwpw; steepest_descent; time_step 1.0e-2; end; end; task pspw steepest_descent nwpw; steepest_descent; time_step 1.0e-1; end; end; task pspw steepest_descent nwpw; steepest_descent; time_step 1.0e0; end; end; task pspw steepest_descent =20 -----Original Message----- From: owner-nwchem-developers@emsl.pnl.gov [mailto:owner-nwchem-developers@emsl.pnl.gov] On Behalf Of Jonas Baltrusaitis Sent: Sunday, June 15, 2008 1:10 PM To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] GUI for plane wave? Is there a way to prepare input/visualize plane wave calculations from any sort of GUI? Would ECCE work with setting up periodic calculations? thanks Jonas =20