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huazhorg鐵桿木蟲 (正式寫手)
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[求助]
怎么分析分子動力學模塊cp.x的運算結(jié)果?
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如題。espresso 里example 18 以及隨后的幾個例子就是運用cp.x進行動力學計算。比如18里,對sio2的計算輸入文件sio2.cp.start.in: &control calculation='cp', restart_mode='from_scratch', nstep=20, iprint=20, isave=20, dt=5.0, ndr=90, ndw=91, pseudo_dir='/home/huazhong/espresso/pseudo/', outdir='/home/huazhong/tmp/', / &system ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955, nat=18, ntyp=2, nbnd=48, nspin=1, ecutwfc=20.0, ecutrho=150.0, nr1b=16, nr2b=16, nr3b=16, qcutz=150., q2sigma=2.0, ecfixed=16.0, / &electrons electron_dynamics='damp', electron_damping=0.2, startingwfc='random', ampre=0.01, emass=700., emass_cutoff=3., / &ions ion_dynamics='none', ion_radius(1)=1.0, ion_radius(2)=1.0, / ATOMIC_SPECIES O 16.00 O.pz-rrkjus.UPF Si 28.00 Si.pz-vbc.UPF ATOMIC_POSITIONS O 3.18829368 14.83237039 1.22882961 O 7.83231469 6.78704039 1.22882961 O 2.07443467 5.99537992 4.73758250 O 6.72031366 14.04231898 4.73758250 O 3.96307134 11.26989826 7.87860582 O 8.60802134 3.22295920 7.87860582 O 3.96307134 4.81915267 9.14625133 O 8.60802134 12.86448267 9.14625133 O 3.18736469 1.25668055 5.58029607 O 7.83324368 9.30201055 5.58029607 O 2.07536366 10.09206195 2.07358613 O 6.71938467 2.04673195 2.07358613 Si 0.28891589 8.04533000 3.40456284 Si 4.93386589 0.00000000 3.40456284 Si 2.13389003 12.27717358 -0.04188031 Si 6.77884003 4.23184358 -0.04188031 Si 2.13389003 3.81348642 6.85202747 Si 6.77884003 11.85881642 6.8520274 這個輸入文件可以用xcrysden查看結(jié)構(gòu)。其對應的輸出文件為sio2.cp.start.out,可是這個輸出文件用xcrysden不能查看結(jié)構(gòu),運行完后幾何結(jié)構(gòu)變成什么樣了,也不知道。那么怎么分析這個輸出文件?請各位仁兄、大俠前來指點。(輸出文件sio2.cp.start.out見附件)[ Last edited by huazhorg on 2012-11-27 at 22:06 ] |
至尊木蟲 (職業(yè)作家)
鐵桿木蟲 (正式寫手)
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謝謝侯老師,很高興得到您的指點?戳艘恍┙坛,似乎略有點明白。它的優(yōu)化坐標不是放在out文件里,而是放在outdir里一個‘prefix’.pos文件里吧,比如我算了一個水分子的優(yōu)化,它的坐標是不是這個文件: 150 0.01456168 0.500990E+01 0.500990E+01 0.500000E+01 0.675162E+01 0.468700E+01 0.509543E+01 0.481703E+01 0.681514E+01 0.494747E+01 160 0.01577113 0.500990E+01 0.500990E+01 0.500000E+01 0.653486E+01 0.438670E+01 0.541771E+01 0.495464E+01 0.677315E+01 0.477299E+01 170 0.01698057 0.500990E+01 0.500990E+01 0.500000E+01 0.650987E+01 0.424898E+01 0.556919E+01 0.502422E+01 0.677687E+01 0.469369E+01 180 0.01819001 0.500990E+01 0.500990E+01 0.500000E+01 0.652258E+01 0.419161E+01 0.564499E+01 0.507221E+01 0.679087E+01 0.465831E+01 190 0.01939945 0.500990E+01 0.500990E+01 0.500000E+01 0.653114E+01 0.418351E+01 0.567759E+01 0.511155E+01 0.680055E+01 0.464628E+01 200 0.02060889 0.500990E+01 0.500990E+01 0.500000E+01 0.653185E+01 0.420141E+01 0.568724E+01 0.514636E+01 0.680329E+01 0.464624E+01 210 0.02181834 0.500990E+01 0.500990E+01 0.500000E+01 0.653089E+01 0.422882E+01 0.568727E+01 0.517752E+01 0.680156E+01 0.465167E+01 220 0.02302778 0.500990E+01 0.500990E+01 0.500000E+01 0.653328E+01 0.425626E+01 0.568513E+01 0.520506E+01 0.679849E+01 0.465888E+01 230 0.02423722 0.500990E+01 0.500990E+01 0.500000E+01 0.654017E+01 0.427980E+01 0.568387E+01 0.522899E+01 0.679605E+01 0.466601E+01 240 0.02544666 0.500990E+01 0.500990E+01 0.500000E+01 0.654995E+01 0.429893E+01 0.568389E+01 0.524946E+01 0.679487E+01 0.467228E+01 250 0.02665611 0.500990E+01 0.500990E+01 0.500000E+01 0.656023E+01 0.431446E+01 0.568456E+01 0.526672E+01 0.679468E+01 0.467751E+01 260 0.02786555 0.500990E+01 0.500990E+01 0.500000E+01 0.656927E+01 0.432735E+01 0.568528E+01 0.528110E+01 0.679498E+01 0.468180E+01 270 0.02907499 0.500990E+01 0.500990E+01 0.500000E+01 0.657642E+01 0.433824E+01 0.568574E+01 0.529294E+01 0.679531E+01 0.468528E+01 280 0.03028443 0.500990E+01 0.500990E+01 0.500000E+01 0.658176E+01 0.434747E+01 0.568594E+01 0.530259E+01 0.679548E+01 0.468808E+01 290 0.03149387 0.500990E+01 0.500990E+01 0.500000E+01 0.658574E+01 0.435520E+01 0.568601E+01 0.531038E+01 0.679547E+01 0.469031E+01 300 0.03270332 0.500990E+01 0.500990E+01 0.500000E+01 0.658877E+01 0.436158E+01 0.568607E+01 0.531662E+01 0.679534E+01 0.469205E+01 310 0.03391276 0.500990E+01 0.500990E+01 0.500000E+01 0.659119E+01 0.436678E+01 0.568619E+01 0.532158E+01 0.679517E+01 0.469337E+01 320 0.03512220 0.500990E+01 0.500990E+01 0.500000E+01 0.659315E+01 0.437096E+01 0.568638E+01 0.532550E+01 0.679501E+01 0.469434E+01 330 0.03633164 0.500990E+01 0.500990E+01 0.500000E+01 0.659475E+01 0.437434E+01 0.568664E+01 0.532858E+01 0.679489E+01 0.469502E+01 340 0.03754108 0.500990E+01 0.500990E+01 0.500000E+01 0.659604E+01 0.437706E+01 0.568694E+01 0.533098E+01 0.679480E+01 0.469545E+01 這個坐標是不是它的優(yōu)化過程?另外怎么可視化這個過程呢,是不是要寫個腳本把它轉(zhuǎn)化成xyz的格式,然后再用xmakemol等這樣的小工具來看優(yōu)化過程?感覺這樣好麻煩呢。。 |
至尊木蟲 (職業(yè)作家)
鐵桿木蟲 (正式寫手)
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謝謝侯老師!我先用cp.x進行了優(yōu)化,然后用cppp.x處理數(shù)據(jù),但是cppp.x沒有一次能運行成功,多次修改里的參數(shù)也不行,這是cppp.x的輸入文件,請您幫我診斷一下: &inputpp outdir = './tmp/', prefix = 'h2o_mol', fileout = 'h2o_mol_dens', output = 'xsf', ndr=51, lcharge=.TRUE., atomic_number(1)=8 atomic_number(2)=1 / 運行結(jié)果總是為: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cppp : error # 1 IONS not found in data-file.xml %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... 這是怎么回事? |
鐵桿木蟲 (正式寫手)
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我是按照這上面的步驟操作的,怎么也會出錯: http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_cp.html (運行例子也是下載這個頁面上的。) |
至尊木蟲 (職業(yè)作家)
鐵桿木蟲 (正式寫手)
鐵桿木蟲 (正式寫手)
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h2o_mol1.in,h2o_mol2.in,h2o_mol3.in,h2o_mol.cp-dens.in這幾個都能正常運行,到最后用cppp.x 運行h2o_mol.cppp-dens.in就出錯了,好奇怪。。。 這是h2o_mol.cp-dens.in的內(nèi)容: &CONTROL title = ' Water Molecule ', calculation = 'cp', restart_mode = 'restart', ndr = 51, ndw = 51, nstep = 50, iprint = 10, isave = 100, tstress = .FALSE., tprnfor = .TRUE., dt = 4.0d0, etot_conv_thr = 1.d-9, ekin_conv_thr = 1.d-4, prefix = 'h2o_mol' disk_io='high' ! to get the charge density pseudo_dir='./', outdir='./tmp/' / &SYSTEM ibrav = 14, celldm(1) = 10.0, celldm(2) = 1.0, celldm(3) = 1.0, celldm(4) = 0.0, celldm(5) = 0.0, celldm(6) = 0.0, nat = 3, ntyp = 2, ecutwfc = 70.0, / &ELECTRONS emass = 300.d0, emass_cutoff = 2.5d0, orthogonalization = 'ortho', electron_dynamics = 'damp', / &IONS ion_dynamics = 'none', ion_temperature = 'not_controlled', tranp(1) = .FALSE. tranp(2) = .TRUE. amprp(2) = 0.1 / ATOMIC_SPECIES O 16.0d0 O.BLYP.UPF H 1.00d0 H.fpmd.UPF ATOMIC_POSITIONS (bohr) O 5.0099 5.0099 5.0000 0 0 0 H 6.8325 4.7757 4.9999 1 1 1 H 4.7757 6.8325 4.9998 1 1 1 |
鐵桿木蟲 (正式寫手)
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