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[交流]
【求助】DL_POLY的config文件如何生成?? 已有9人參與
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我想模擬聚合物在金屬團(tuán)簇表面的吸附,想請(qǐng)教大家這樣的體系的config文件如何生成? 另外我把手冊(cè)已經(jīng)看了一遍,但是希望運(yùn)行一下.有么有人根據(jù)手冊(cè)的算例給寫一個(gè)模擬過(guò)程,給傳一個(gè)謝謝!! |

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這是我運(yùn)行了100步停止的輸出文件.......... ************** stfc/ccp5 program library package daresbury laboratory molecular D L _ P O L Y dynamics program for large systems authors: i.t.todorov & w.smith ************** version 3.09.4 / september 2008 ************** Execution on 8 node(s) ****** node/domain decomposition (x,y,z): 2 2 2 link-cell decomposition 1 (x,y,z): 1 1 1 warning issued 100 *** warning - employed link cell algorithm has a link cell dimension is < 4 !!! *** *** DL_POLY_3 RUNNING IN LOW EFFICIENCY MODE !!! *** ********************************************************************************************************************************** ********************************************************************************************************************************** ********************************************************************************************************************************** ************************ DL_POLY TEST CASE 2: Al with Sutton-Chen potential ************************ ********************************************************************************************************************************** ********************************************************************************************************************************** ********************************************************************************************************************************** SIMULATION CONTROL PARAMETERS simulation temperature (K) 3.0000E+02 simulation pressure (katms) 0.0000E+00 Integration : Leapfrog Verlet Ensemble : NVT Berendsen thermostat relaxation time (ps) 1.0000E-01 no index (reading in CONFIG) option on selected number of timesteps 10000 warning issued 36 *** warning - DL_POLY_2 directive 'mult(iple timestep)' defaulted to *** *** DL_POLY_3 'infrequent k-space SPME evaluation' directive *** temperature scaling on (during equilibration) temperature scaling interval 10 data printing interval 50 data stacking interval 100 statistics file interval 10 trajectory file option on trajectory file start 1000 trajectory file interval 100 trajectory file info key 0 density variation allowance (%) 3.0000E+01 real space cutoff (Ang) 1.3000E+01 warning issued 35 *** warning - redundant directive delr ignored *** vdw cutoff (Ang) 1.0000E+01 warning issued 33 *** warning - redundant directive quaternion ignored *** user allocated job time (s) 1.8000E+04 job closure time (s) 3.0000E+02 clean start requested Electrostatics switched off!!! fixed simulation timestep (ps) 1.0000E-04 data dumping interval 1000 SYSTEM SPECIFICATION energy units = kJ/mol number of molecular types 1 molecular species type 1 name of species: butanethiol number of molecules 40 number of atoms/sites 5 atomic characteristics: site name mass charge repeat freeze 1 C1 15.035000 0.000000 1 0 2 C2 14.027000 0.000000 1 0 3 C2 14.027000 0.000000 1 0 4 C2 14.027000 0.000000 1 0 5 S14 33.068000 0.000000 1 0 number of chemical bonds 4 chemical bond details: unit key index index parameters 1 harm 1 2 500000.000000 1.540000 0.000000 0.000000 2 harm 2 3 500000.000000 1.540000 0.000000 0.000000 3 harm 3 4 500000.000000 1.540000 0.000000 0.000000 4 harm 4 5 500000.000000 1.820000 0.000000 0.000000 number of bond angles 3 bond angle details: unit key index index index f-const angle 1 harm 1 2 3 0.158000 114.400000 0.000000 0.000000 2 harm 2 3 4 0.158000 114.400000 0.000000 0.000000 3 harm 3 4 5 0.158000 114.400000 0.000000 0.000000 number of dihedral angles 2 dihedral angle details: unit key index index index index f-const angle trig 1-4 elec 1-4 vdw 1 cos3 1 2 3 4 5.904600 -1.134000 13.160800 0.000000 0.000000 0.000000 0.000000 2 cos3 2 3 4 5 5.904600 -1.134000 13.160800 0.000000 0.000000 0.000000 0.000000 number of specified vdw potentials 6 pair atom 1 atom 2 key parameters 1 C1 C1 lj 0.814600 3.750000 0.000000 0.000000 0.000000 2 C2 C2 lj 0.382000 3.950000 0.000000 0.000000 0.000000 3 S14 S14 lj 1.046000 4.450000 0.000000 0.000000 0.000000 4 C1 C2 lj 0.558000 3.850000 0.000000 0.000000 0.000000 5 C1 S14 lj 0.923000 4.100000 0.000000 0.000000 0.000000 6 C2 S14 lj 0.633000 4.200000 0.000000 0.000000 0.000000 configuration file name: input-turn-config selected image convention 1 simulation cell vectors 30.0000000000 0.0000000000 0.0000000000 0.0000000000 30.0000000000 0.0000000000 0.0000000000 0.0000000000 30.0000000000 system volume 27000.0000000 long-range correction for: vdw energy -0.317042E+02 : vdw pressure -0.384247E-01 degrees of freedom break-down list ---------------------------------- all particles 600 centre of mass -3 non-periodicity 0 frozen 0 shell-pseudo 0 constrained 0 ---------------------------------- total (real) 597 sample of starting configuration on node zero i x(i) y(i) z(i) vx(i) vy(i) vz(i) 1 -5.3460E+00 -4.3530E+00 -5.8400E+00 5.3187E+00 1.6975E+00 -3.5250E+00 3 -6.9280E+00 -5.8680E+00 -7.2810E+00 4.2182E+00 2.1674E+00 -2.8500E+00 5 -4.4550E+00 -2.7160E+00 -5.8810E+00 -5.2572E+00 -2.0707E-01 2.9524E+00 14 -1.6820E+00 -9.4200E-01 -2.2340E+00 6.7830E+00 1.7340E-01 -6.5509E+00 71 -7.3000E-01 -3.3240E+00 -6.1350E+00 -4.3704E+00 -3.9108E-01 -3.1877E+00 73 -4.1200E-01 -5.9120E+00 -5.8400E+00 3.1470E-01 -4.4419E+00 1.7874E-03 141 -7.2950E+00 -2.7620E+00 -1.3680E+00 1.6247E+00 5.0967E+00 -2.4214E+00 143 -9.5090E+00 -1.8080E+00 -2.0280E+00 4.3821E+00 -6.1615E+00 2.2758E+00 145 -6.0100E+00 -4.0350E+00 -1.7720E+00 1.8533E+00 -3.4578E+00 1.5776E+00 181 -7.6030E+00 -7.9500E-01 -6.0470E+00 4.2181E+00 -6.2552E-01 -1.5844E-02 185 -8.5010E+00 -2.3300E+00 -6.1790E+00 -7.0193E-01 1.5605E+00 -1.0806E+00 187 -3.6970E+00 -7.7220E+00 -2.4700E+00 -3.8794E+00 -3.1952E+00 6.3163E+00 189 -4.7470E+00 -9.9870E+00 -2.7590E+00 1.7072E+00 -1.3292E+01 -5.6002E+00 ---------------------------------------------------------------------------------------------------------------------------------- step eng_tot temp_tot eng_cfg eng_src eng_cou eng_bnd eng_ang eng_dih eng_tet time(ps) eng_pv temp_rot vir_cfg vir_src vir_cou vir_bnd vir_ang vir_con vir_tet cpu (s) volume temp_shl eng_shl vir_shl alpha beta gamma vir_pmf press ---------------------------------------------------------------------------------------------------------------------------------- 0 1.2483E+08 3.0000E+02 1.2483E+08 2.5787E+06 0.0000E+00 1.2225E+08 6.1460E+00 7.8775E+02 0.0000E+00 0.00000 1.1556E+07 0.0000E+00 3.3981E+08 -3.1072E+07 0.0000E+00 3.7088E+08 0.0000E+00 0.0000E+00 0.0000E+00 0.1 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -6.8752E+04 ---------------------------------------------------------------------------------------------------------------------------------- time elapsed since job start: 0.063 sec ---------------------------------------------------------------------------------------------------------------------------------- step eng_tot temp_tot eng_cfg eng_src eng_cou eng_bnd eng_ang eng_dih eng_tet time(ps) eng_pv temp_rot vir_cfg vir_src vir_cou vir_bnd vir_ang vir_con vir_tet cpu (s) volume temp_shl eng_shl vir_shl alpha beta gamma vir_pmf press ---------------------------------------------------------------------------------------------------------------------------------- 1 1.2628E+08 5.8520E+05 1.2483E+08 2.5787E+06 0.0000E+00 1.2225E+08 6.1460E+00 7.8775E+02 0.0000E+00 0.00010 1.3976E+07 0.0000E+00 3.3981E+08 -3.1072E+07 0.0000E+00 3.7088E+08 0.0000E+00 0.0000E+00 0.0000E+00 0.1 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -6.8165E+04 rolling 1.2628E+08 5.8520E+05 1.2483E+08 2.5787E+06 0.0000E+00 1.2225E+08 6.1460E+00 7.8775E+02 0.0000E+00 averages 1.3976E+07 0.0000E+00 3.3981E+08 -3.1072E+07 0.0000E+00 3.7088E+08 0.0000E+00 0.0000E+00 0.0000E+00 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -6.8165E+04 ---------------------------------------------------------------------------------------------------------------------------------- 50 1.2434E+08 1.5181E+07 8.6666E+07 2.4960E+05 0.0000E+00 8.6416E+07 7.6470E+00 7.7596E+02 0.0000E+00 0.00500 5.6513E+07 0.0000E+00 2.7884E+08 -3.0316E+06 0.0000E+00 2.8188E+08 0.0000E+00 0.0000E+00 0.0000E+00 0.1 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -4.1171E+04 rolling 1.2467E+08 3.0763E+07 4.8317E+07 6.5331E+05 0.0000E+00 4.7662E+07 1.0349E+01 7.4649E+02 0.0000E+00 averages 1.2292E+08 0.0000E+00 1.5795E+08 -7.8918E+06 0.0000E+00 1.6584E+08 0.0000E+00 0.0000E+00 0.0000E+00 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -1.0626E+03 ---------------------------------------------------------------------------------------------------------------------------------- 100 1.1977E+08 2.5558E+07 5.6340E+07 2.4380E+05 0.0000E+00 5.6096E+07 1.0932E+01 7.8518E+02 0.0000E+00 0.01000 8.7243E+07 0.0000E+00 2.2445E+08 -2.9529E+06 0.0000E+00 2.2740E+08 0.0000E+00 0.0000E+00 0.0000E+00 0.2 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -1.9744E+04 rolling 1.2318E+08 3.2070E+07 4.3587E+07 4.5891E+05 0.0000E+00 4.3127E+07 9.5630E+00 7.4649E+02 0.0000E+00 averages 1.2321E+08 0.0000E+00 1.5909E+08 -5.5496E+06 0.0000E+00 1.6464E+08 0.0000E+00 0.0000E+00 0.0000E+00 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 1.9383E+01 ---------------------------------------------------------------------------------------------------------------------------------- DL_POLY_3 terminated due to error 445 |

木蟲 (著名寫手)

木蟲 (著名寫手)
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難處在于,誰(shuí)肯費(fèi)這個(gè)時(shí)間教你呢?你多少也應(yīng)該自己學(xué)一些,然后就某一點(diǎn)難以解決之處來(lái)提問(wèn)。如果叫人家給你寫個(gè)通盤的教程,給你個(gè)完整的例子,換了你,你愿意干么?就算你愿意,你有那個(gè)時(shí)間么?大家都很忙啊。 Config文件如何生成,手冊(cè)上講得非常之詳細(xì),你自己試著下手弄一下,哪里不懂可以提問(wèn),這樣好一些,也學(xué)得比較快。關(guān)鍵是要?jiǎng)邮职 ? |
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