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missingwudi新虫 (初入文坛)
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[求助]
利用探针probe分子计算CH4的emap,出现报错
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我想模拟OH对CH4的的影响，把CH4看做四面体构型，先前的想法是分别计算C原子和H原子的emap，结果和文献中的值差很大。后来想利用MuSic中的探针probe计算，一直运行不成功，报错。下面将我的输入文件贴在下面： 原子文件： Patom.atm ##### Basic Atom Information Atom_Name: Patom Atom_Symbol: P Atom_SS_Charge: 0.0 Atom_SZ_Charge: 0.0 Atom_Mass: 16.0 Atom_Valency: 0 Latom.atm ##### Basic Atom Information Atom_Name: Latom Atom_Symbol: L Atom_SS_Charge: 0.0 Atom_SZ_Charge: 0.0 Atom_Mass: 16.0 Atom_Valency: 0 分子文件： A_C_OH.mol Molecule_Name: A_C_OH Coord_Info: Listed Cartesian None 1920 # number of atoms in molecule 1 9.006 11.076 7.512 Latom 0.0 0 0 2 8.243 10.386 6.530 Latom 0.0 0 0 3 8.463 10.644 5.150 Latom 0.0 0 0 4 9.446 11.592 4.752 Latom 0.0 0 0 5 10.209 12.282 5.734 Latom 0.0 0 0 6 9.989 12.023 7.114 Latom 0.0 0 0 7 10.752 12.718 8.101 Latom 0.0 0 0 8 11.710 13.657 7.680 Latom 0.0 0 0 9 11.945 13.890 6.325 Latom 0.0 0 0 10 11.198 13.229 5.334 Latom 0.0 0 0 11 8.784 10.818 8.898 Latom 0.0 0 0 12 9.551 11.513 9.847 Latom 0.0 0 0 13 10.512 12.441 9.457 Latom 0.0 0 0 14 7.808 9.878 9.263 Latom 0.0 0 0 15 7.060 9.202 8.302 Latom 0.0 0 0 16 7.256 9.436 6.930 Latom 0.0 0 0 17 7.698 9.952 4.163 Latom 0.0 0 0 18 6.733 9.022 4.583 Latom 0.0 0 0 19 6.517 8.769 5.939 Latom 0.0 0 0 20 9.668 11.850 3.366 Latom 0.0 0 0 21 8.901 11.156 2.417 Latom 0.0 0 0 22 7.938 10.228 2.806 Latom 0.0 0 0 23 11.393 13.464 3.962 Latom 0.0 0 0 24 10.645 12.790 3.000 Latom 0.0 0 0 25 12.417 14.425 8.587 Latom -1.0 0 0 26 12.977 14.752 6.001 Latom -1.0 0 0 27 9.400 11.317 11.204 Latom -1.0 0 0 28 11.231 13.070 10.452 Latom -1.0 0 0 29 7.558 9.595 10.589 Latom -1.0 0 0 30 6.130 8.302 8.776 Latom -1.0 0 0 31 5.977 8.337 3.657 Latom -1.0 0 0 32 5.557 7.845 6.291 Latom -1.0 0 0 33 9.080 11.372 1.067 Latom -1.0 0 0 34 7.246 9.607 1.788 Latom -1.0 0 0 35 12.322 14.381 3.520 Latom -1.0 0 0 36 10.917 13.099 1.684 Latom -1.0 0 0 37 12.513 15.309 8.215 Latom 1.0 0 0 38 13.684 14.621 6.642 Latom 1.0 0 0 39 10.041 11.905 11.623 Latom 1.0 0 0 40 11.856 13.656 10.002 Latom 1.0 0 0 41 8.166 10.153 11.097 Latom 1.0 0 0 42 6.203 8.338 9.738 Latom 1.0 0 0 43 6.271 8.646 2.789 Latom 1.0 0 0 44 5.557 7.812 7.257 Latom 1.0 0 0 45 9.779 12.039 0.997 Latom 1.0 0 0 46 7.603 9.974 0.971 Latom 1.0 0 0 47 12.726 14.760 4.313 Latom 1.0 0 0 48 11.614 13.766 1.712 Latom 1.0 0 0 49 26.210 7.177 39.402 Latom 0.0 0 0 50 27.020 8.261 39.841 Latom 0.0 0 0 51 26.474 9.571 39.913 Latom 0.0 0 0 52 25.119 9.798 39.547 Latom 0.0 0 0 53 24.309 8.714 39.108 Latom 0.0 0 0 54 24.855 7.404 39.036 Latom 0.0 0 0 55 24.044 6.316 38.592 Latom 0.0 0 0 56 22.710 6.569 38.227 Latom 0.0 0 0 57 22.166 7.850 38.324 Latom 0.0 0 0 58 22.947 8.941 38.745 Latom 0.0 0 0 59 26.759 5.862 39.328 Latom 0.0 0 0 60 25.937 4.810 38.891 Latom 0.0 0 0 61 24.611 5.032 38.531 Latom 0.0 0 0 62 28.099 5.666 39.695 Latom 0.0 0 0 63 28.892 6.726 40.125 Latom 0.0 0 0 64 28.380 8.033 40.208 Latom 0.0 0 0 65 27.286 10.659 40.354 Latom 0.0 0 0 66 28.622 10.408 40.709 Latom 0.0 0 0 67 29.158 9.121 40.638 Latom 0.0 0 0 68 24.570 11.113 39.621 Latom 0.0 0 0 69 25.391 12.165 40.057 Latom 0.0 0 0 70 26.718 11.944 40.416 Latom 0.0 0 0 71 22.436 10.247 38.826 Latom 0.0 0 0 72 23.229 11.309 39.254 Latom 0.0 0 0 73 21.901 5.577 37.705 Latom -1.0 0 0 74 20.819 7.989 38.044 Latom -1.0 0 0 75 26.390 3.511 38.796 Latom -1.0 0 0 76 23.869 3.943 38.126 Latom -1.0 0 0 77 28.672 4.413 39.640 Latom -1.0 0 0 78 30.193 6.417 40.460 Latom -1.0 0 0 79 29.432 11.436 41.138 Latom -1.0 0 0 80 30.474 8.935 40.999 Latom -1.0 0 0 81 24.906 13.452 40.145 Latom -1.0 0 0 82 27.429 13.050 40.829 Latom -1.0 0 0 83 21.134 10.527 38.471 Latom -1.0 0 0 84 22.626 12.549 39.294 Latom -1.0 0 0 85 21.357 5.970 37.014 Latom 1.0 0 0 86 20.367 7.201 38.365 Latom 1.0 0 0 87 25.637 2.996 38.482 Latom 1.0 0 0 88 22.981 4.277 37.938 Latom 1.0 0 0 89 27.976 3.818 39.325 Latom 1.0 0 0 90 30.279 5.467 40.314 Latom 1.0 0 0 91 28.888 12.234 41.119 Latom 1.0 0 0 92 30.655 7.993 40.883 Latom 1.0 0 0 93 23.981 13.406 39.858 Latom 1.0 0 0 94 26.811 13.789 40.777 Latom 1.0 0 0 ..................... 1867 8.148 10.874 23.574 Latom 1.0 0 0 1868 9.584 15.018 24.962 Latom 1.0 0 0 1869 3.214 9.770 22.360 Latom 1.0 0 0 1870 6.155 9.368 22.796 Latom 1.0 0 0 1871 -0.454 13.447 22.705 Latom 1.0 0 0 1872 0.800 10.772 22.191 Latom 1.0 0 0 1873 31.499 15.151 10.962 Latom 0.0 0 0 1874 30.385 14.325 10.650 Latom 0.0 0 0 1875 29.597 14.601 9.500 Latom 0.0 0 0 1876 29.922 15.704 8.664 Latom 0.0 0 0 1877 31.036 16.531 8.977 Latom 0.0 0 0 1878 31.825 16.254 10.126 Latom 0.0 0 0 1879 32.941 17.086 10.443 Latom 0.0 0 0 1880 33.235 18.176 9.604 Latom 0.0 0 0 1881 32.477 18.431 8.461 Latom 0.0 0 0 1882 31.364 17.636 8.134 Latom 0.0 0 0 1883 32.291 14.874 12.117 Latom 0.0 0 0 1884 33.385 15.706 12.404 Latom 0.0 0 0 1885 33.703 16.787 11.585 Latom 0.0 0 0 1886 31.948 13.780 12.926 Latom 0.0 0 0 1887 30.858 12.969 12.620 Latom 0.0 0 0 1888 30.059 13.218 11.490 Latom 0.0 0 0 1889 28.478 13.772 9.186 Latom 0.0 0 0 1890 28.179 12.689 10.029 Latom 0.0 0 0 1891 28.953 12.417 11.158 Latom 0.0 0 0 1892 29.130 15.981 7.509 Latom 0.0 0 0 1893 28.037 15.150 7.223 Latom 0.0 0 0 1894 27.717 14.070 8.042 Latom 0.0 0 0 1895 30.566 17.885 7.006 Latom 0.0 0 0 1896 29.474 17.076 6.700 Latom 0.0 0 0 1897 34.246 19.069 9.905 Latom -1.0 0 0 1898 32.899 19.459 7.639 Latom -1.0 0 0 1899 34.201 15.503 13.497 Latom -1.0 0 0 1900 34.801 17.546 11.929 Latom -1.0 0 0 1901 32.683 13.472 14.051 Latom -1.0 0 0 1902 30.615 11.923 13.484 Latom -1.0 0 0 1903 27.106 11.869 9.754 Latom -1.0 0 0 1904 28.612 11.342 11.948 Latom -1.0 0 0 1905 27.243 15.378 6.119 Latom -1.0 0 0 1906 26.622 13.323 7.664 Latom -1.0 0 0 1907 30.826 18.948 6.167 Latom -1.0 0 0 1908 28.758 17.413 5.570 Latom -1.0 0 0 1909 33.945 19.951 9.661 Latom 1.0 0 0 1910 33.862 19.465 7.642 Latom 1.0 0 0 1911 34.867 16.201 13.456 Latom 1.0 0 0 1912 34.880 18.229 11.248 Latom 1.0 0 0 1913 33.388 14.136 14.096 Latom 1.0 0 0 1914 31.300 11.983 14.161 Latom 1.0 0 0 1915 26.704 12.215 8.946 Latom 1.0 0 0 1916 29.257 11.320 12.667 Latom 1.0 0 0 1917 27.616 16.159 5.683 Latom 1.0 0 0 1918 26.291 13.738 6.859 Latom 1.0 0 0 1919 31.595 19.402 6.540 Latom 1.0 0 0 1920 29.195 18.194 5.209 Latom 1.0 0 0 Molecule_DOF: 6 Fundcell_Info: Listed 44.979 44.979 44.979 # unit cell edge lengths 90.00000 90.00000 90.00000 # unit cell angles 0.00000 0.00000 0.00000 # origin of unit cell 44.979 44.979 44.979 # effective bound box size Probe.mol # Generated molecule file Molecule_Name: Probe CHARGED Coord_Info: Listed Cartesian Rigid 1 # number of atoms in molecule 1 0.50000 0.50000 0.5000 Patom 1.0 0 0 Molecule_DOF: 3 原子与原子文件 ## This is generated LJ interactions Latom Patom LJ SIG@3.69937 EPS@125.80750 LOCUT@0.1 HICUT@5.9 分子分子文件 A_C_OH A_C_OH NCOUL OFF A_C_OH A_C_OH COUL OFF Probe A_C_OH NCOUL OFF Probe A_C_OH COUL SUM FAST FIXED EWALD SFACTOR KMAX@15 KAPPA@6.7 LOCUT@1e-10 Probe Probe NCOUL OFF Probe Probe COUL OFF 分子作用文件 Intra: A_C_OH Intra: Probe 控制文件 ------ General Information ------------------------------------------ Probe_C in A_C_OH 1 # No. of iterations 1 # No. of steps between writes to output/log file 1 # No. of steps between writes to crash file 1 # No. of steps between writes to config. file 2 # Start numbering simulations from . 1892134 # Iseeed 4 # specifies contents of config file, Probe.empa.res # Restart File to write to Probe.emap.con # Configuration File ------ Atomic Types -------------------------------------------------- 2 # number of atomic types Patom Patom.atm Latom Latom.atm ------ Molecule Types ------------------------------------------------- 2 # number of sorbate types Probe Probe.mol A_C_OH # sorbate A_C_OH.mol # sorbate coordinates file ------ Simulation Cell Information -------------------------------------- A_C_OH # Fundamental cell type 1, 1, 1 # No. of unit cells in x, y, z direction 1, 1, 1 # (1 = Periodic) in x, y, z ------ Forcefield Information ------------------------------------------- BASIC SPC atom_atom_file # atom-atom interaction file spc_spc_file_emap # sorbate-sorbate interaction file intramolecular_file # intramolecular interaction file/specification ------ Mapmaker Information -------------------------------------------- 1 # Number of maps to make A_C_OH # Sorbate to map Probe # Sorbate to Probe_C map with COUL EWALD # Interaction type to map 0.25 # Approximate grid spacing (Ang) 100.0 # High end potential cutoff (kJ/mol) AUTO # Map filename or AUTO ------ Configuration Initialization ------------------------------------- Probe # Sorbate_Type GCMC NULL # Source Filename A_C_OH # Sorbate_Type Fixed NULL # Source Filena 报错： ./run-mapmake.sh: line 1: o!/bin/sh: No such file or directory setting environment variables ---- CURRENT MUSIC OUTPUT -------------------- molecule.F90 : 637 WARNING: Probe is not charge neutral (1.00) ewald.F90: 187 WARNING: nkmax is hard coded to 50000 Total number of K vectors calculated: 932 Total number of atoms used for K vec: 1920 mapmaker.F90: 181 Molecule to map Probe must have a FIXED configuration |
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