git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12769 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
111
tools/i-pi/examples/tutorial/tutorial-1/our_ref.pdb
Executable file
111
tools/i-pi/examples/tutorial/tutorial-1/our_ref.pdb
Executable file
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TITLE Traj: positions{angstrom} Step: 0 Bead: 1
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CRYST1 17.847 17.847 17.847 90.00 90.00 90.00 P 1 1
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ATOM 1 H2 1 1 0.147 0.132 0.114 0.00 0.00 0
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ATOM 2 H2 1 1 -0.125 2.943 3.188 0.00 0.00 0
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ATOM 3 H2 1 1 3.042 2.937 0.107 0.00 0.00 0
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ATOM 4 H2 1 1 2.976 -0.148 2.960 0.00 0.00 0
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ATOM 5 H2 1 1 -0.229 -0.030 5.923 0.00 0.00 0
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ATOM 6 H2 1 1 0.094 2.999 8.915 0.00 0.00 0
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ATOM 7 H2 1 1 2.954 2.895 5.910 0.00 0.00 0
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ATOM 8 H2 1 1 2.892 -0.155 8.870 0.00 0.00 0
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ATOM 9 H2 1 1 -0.048 0.087 11.901 0.00 0.00 0
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ATOM 10 H2 1 1 0.017 2.947 14.955 0.00 0.00 0
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ATOM 11 H2 1 1 2.979 2.989 11.875 0.00 0.00 0
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ATOM 12 H2 1 1 2.976 0.114 14.794 0.00 0.00 0
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ATOM 13 H2 1 1 -0.053 5.852 -0.165 0.00 0.00 0
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ATOM 14 H2 1 1 0.006 8.858 3.040 0.00 0.00 0
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ATOM 15 H2 1 1 3.041 8.951 -0.096 0.00 0.00 0
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ATOM 16 H2 1 1 3.007 5.879 2.876 0.00 0.00 0
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ATOM 17 H2 1 1 0.057 5.910 6.036 0.00 0.00 0
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ATOM 18 H2 1 1 -0.097 8.867 8.804 0.00 0.00 0
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ATOM 19 H2 1 1 2.832 8.766 5.719 0.00 0.00 0
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ATOM 20 H2 1 1 3.148 5.956 8.964 0.00 0.00 0
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ATOM 21 H2 1 1 0.031 5.974 11.932 0.00 0.00 0
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ATOM 22 H2 1 1 0.124 8.972 14.723 0.00 0.00 0
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ATOM 23 H2 1 1 2.998 8.861 11.952 0.00 0.00 0
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ATOM 24 H2 1 1 2.971 5.943 14.914 0.00 0.00 0
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ATOM 25 H2 1 1 0.009 11.770 0.089 0.00 0.00 0
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ATOM 26 H2 1 1 0.015 14.931 2.992 0.00 0.00 0
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ATOM 27 H2 1 1 2.924 14.889 0.062 0.00 0.00 0
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ATOM 28 H2 1 1 2.832 11.918 3.162 0.00 0.00 0
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ATOM 29 H2 1 1 -0.097 11.885 6.105 0.00 0.00 0
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ATOM 30 H2 1 1 0.169 14.731 8.889 0.00 0.00 0
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ATOM 31 H2 1 1 2.877 14.750 5.921 0.00 0.00 0
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ATOM 32 H2 1 1 3.078 12.038 8.936 0.00 0.00 0
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ATOM 33 H2 1 1 0.019 12.011 11.885 0.00 0.00 0
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ATOM 34 H2 1 1 0.139 14.848 14.841 0.00 0.00 0
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ATOM 35 H2 1 1 2.904 14.835 12.020 0.00 0.00 0
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ATOM 36 H2 1 1 3.083 12.013 14.942 0.00 0.00 0
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ATOM 37 H2 1 1 6.042 0.051 -0.122 0.00 0.00 0
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ATOM 38 H2 1 1 5.911 2.957 2.811 0.00 0.00 0
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ATOM 39 H2 1 1 8.949 3.111 0.013 0.00 0.00 0
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ATOM 40 H2 1 1 8.991 -0.010 2.794 0.00 0.00 0
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ATOM 41 H2 1 1 6.061 0.042 6.018 0.00 0.00 0
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ATOM 42 H2 1 1 6.156 3.002 8.708 0.00 0.00 0
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ATOM 43 H2 1 1 8.922 3.069 5.909 0.00 0.00 0
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ATOM 44 H2 1 1 8.988 0.132 9.006 0.00 0.00 0
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ATOM 45 H2 1 1 5.916 0.157 11.936 0.00 0.00 0
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ATOM 46 H2 1 1 6.011 2.841 14.909 0.00 0.00 0
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ATOM 47 H2 1 1 8.974 2.990 11.906 0.00 0.00 0
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ATOM 48 H2 1 1 8.946 -0.012 14.762 0.00 0.00 0
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ATOM 49 H2 1 1 5.871 5.856 -0.119 0.00 0.00 0
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ATOM 50 H2 1 1 6.164 8.843 3.017 0.00 0.00 0
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ATOM 51 H2 1 1 9.193 8.762 0.076 0.00 0.00 0
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ATOM 52 H2 1 1 8.834 5.965 2.835 0.00 0.00 0
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ATOM 53 H2 1 1 5.987 6.003 5.941 0.00 0.00 0
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ATOM 54 H2 1 1 5.977 8.974 8.839 0.00 0.00 0
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ATOM 55 H2 1 1 9.025 8.846 6.022 0.00 0.00 0
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ATOM 56 H2 1 1 8.848 5.694 9.143 0.00 0.00 0
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ATOM 57 H2 1 1 5.924 6.032 11.865 0.00 0.00 0
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ATOM 58 H2 1 1 6.019 8.827 14.866 0.00 0.00 0
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ATOM 59 H2 1 1 8.835 9.076 11.941 0.00 0.00 0
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ATOM 60 H2 1 1 8.891 6.039 14.895 0.00 0.00 0
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ATOM 61 H2 1 1 5.856 11.998 0.105 0.00 0.00 0
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ATOM 62 H2 1 1 5.828 14.783 2.903 0.00 0.00 0
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ATOM 63 H2 1 1 8.942 14.899 -0.042 0.00 0.00 0
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ATOM 64 H2 1 1 8.930 11.966 3.015 0.00 0.00 0
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ATOM 65 H2 1 1 6.073 11.865 5.912 0.00 0.00 0
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ATOM 66 H2 1 1 6.031 14.891 8.979 0.00 0.00 0
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ATOM 67 H2 1 1 8.972 14.858 5.883 0.00 0.00 0
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ATOM 68 H2 1 1 8.957 11.835 8.967 0.00 0.00 0
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ATOM 69 H2 1 1 5.966 11.882 12.044 0.00 0.00 0
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ATOM 70 H2 1 1 5.947 14.705 14.774 0.00 0.00 0
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ATOM 71 H2 1 1 8.876 14.853 11.951 0.00 0.00 0
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ATOM 72 H2 1 1 8.992 11.917 14.929 0.00 0.00 0
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ATOM 73 H2 1 1 11.946 0.088 -0.028 0.00 0.00 0
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ATOM 74 H2 1 1 11.829 3.081 3.117 0.00 0.00 0
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ATOM 75 H2 1 1 15.004 3.033 -0.008 0.00 0.00 0
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ATOM 76 H2 1 1 14.828 0.120 3.029 0.00 0.00 0
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ATOM 77 H2 1 1 11.906 0.017 5.995 0.00 0.00 0
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ATOM 78 H2 1 1 11.873 2.916 9.016 0.00 0.00 0
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ATOM 79 H2 1 1 14.907 3.062 5.960 0.00 0.00 0
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ATOM 80 H2 1 1 14.948 -0.122 8.864 0.00 0.00 0
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ATOM 81 H2 1 1 11.869 -0.118 11.930 0.00 0.00 0
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ATOM 82 H2 1 1 11.932 2.863 14.979 0.00 0.00 0
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ATOM 83 H2 1 1 14.835 2.976 12.018 0.00 0.00 0
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ATOM 84 H2 1 1 14.852 -0.218 14.783 0.00 0.00 0
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ATOM 85 H2 1 1 11.892 5.990 0.058 0.00 0.00 0
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ATOM 86 H2 1 1 11.816 8.684 2.936 0.00 0.00 0
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ATOM 87 H2 1 1 14.958 8.876 -0.055 0.00 0.00 0
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ATOM 88 H2 1 1 14.840 6.061 2.916 0.00 0.00 0
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ATOM 89 H2 1 1 11.911 5.971 5.726 0.00 0.00 0
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ATOM 90 H2 1 1 11.921 8.947 8.915 0.00 0.00 0
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ATOM 91 H2 1 1 15.032 8.972 5.831 0.00 0.00 0
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ATOM 92 H2 1 1 14.699 5.889 8.931 0.00 0.00 0
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ATOM 93 H2 1 1 11.765 5.844 11.846 0.00 0.00 0
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ATOM 94 H2 1 1 11.983 8.755 14.933 0.00 0.00 0
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ATOM 95 H2 1 1 14.840 8.926 11.947 0.00 0.00 0
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ATOM 96 H2 1 1 14.976 5.712 14.771 0.00 0.00 0
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ATOM 97 H2 1 1 11.824 11.871 -0.007 0.00 0.00 0
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ATOM 98 H2 1 1 11.894 14.840 2.771 0.00 0.00 0
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ATOM 99 H2 1 1 15.039 14.928 0.021 0.00 0.00 0
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ATOM 100 H2 1 1 14.876 11.851 2.910 0.00 0.00 0
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ATOM 101 H2 1 1 11.785 11.934 6.071 0.00 0.00 0
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ATOM 102 H2 1 1 11.937 14.681 8.929 0.00 0.00 0
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ATOM 103 H2 1 1 14.935 14.902 5.873 0.00 0.00 0
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ATOM 104 H2 1 1 14.882 11.944 9.007 0.00 0.00 0
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ATOM 105 H2 1 1 11.941 11.956 11.877 0.00 0.00 0
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ATOM 106 H2 1 1 11.791 14.900 14.955 0.00 0.00 0
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ATOM 107 H2 1 1 14.838 14.947 11.831 0.00 0.00 0
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ATOM 108 H2 1 1 14.891 12.005 15.050 0.00 0.00 0
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END
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110
tools/i-pi/examples/tutorial/tutorial-1/our_ref.xyz
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110
tools/i-pi/examples/tutorial/tutorial-1/our_ref.xyz
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108
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# CELL(abcABC): 17.8469984966 17.8469984966 17.8469984966 90.00000 90.00000 90.00000 Traj: positions Step: 0 Bead: 0
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H2 0.147000137166 0.132000079971 0.114000117173
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H2 -0.125000123837 2.94299788633 3.18800164278
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H2 3.04200165055 2.93700230854 0.107000161039
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H2 2.97599737714 -0.147999752916 2.96000035008
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H2 -0.228999850096 -0.0300000085539 5.92297467609
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H2 0.0939998645211 2.99900071046 8.91499553915
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H2 2.95399948052 2.89500151338 5.91000983444
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H2 2.8920010786 -0.155000238227 8.8700154763
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H2 -0.0480000242697 0.0869999083873 11.900983782
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H2 0.0169999766244 2.94699846603 14.9550242141
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H2 2.97899781192 2.98899926119 11.875001181
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H2 2.97599737714 0.114000117173 14.7939955891
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H2 -0.0529997434675 5.85201201223 -0.165000099964
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H2 0.00600002287786 8.85800315363 3.04000136069
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H2 3.04100150562 8.95097958943 -0.0960001543749
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H2 3.00700186988 5.87900004994 2.87599875977
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H2 0.0569997939979 5.91000983444 6.03600692814
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H2 -0.0969997701246 8.8669991662 8.80397416049
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H2 2.83199767476 8.76597923681 5.71897686163
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H2 3.14800113748 5.95599533399 8.96399734879
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H2 0.0309999947276 5.97398735913 11.9319935665
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H2 0.12399997891 8.97198792467 14.7229800075
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H2 2.99800056553 8.86101946373 11.9519964651
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H2 2.97100194428 5.94297757463 14.9140129803
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H2 0.00899998139907 11.7700124225 0.0890001982411
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H2 0.0150000042769 14.9309995688 2.99199969597
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H2 2.92400042449 14.8889828983 0.0619999894552
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H2 2.83199767476 11.9180232882 3.16199787469
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H2 -0.0969997701246 11.8850026303 6.10501163633
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H2 0.169000150494 14.7310235011 8.88901293814
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H2 2.8769989047 14.7500209629 5.92101672041
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H2 3.07800157614 12.0379877617 8.93600387439
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H2 0.0190000018896 12.010999724 11.8850026303
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H2 0.139000036105 14.8480245822 14.8409865253
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H2 2.90399752595 14.8350068229 12.0199957365
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H2 3.08300230078 12.0130105974 14.9420064547
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H2 6.04198663062 0.050999982791 -0.122000218234
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H2 5.91101527114 2.9569999153 2.81099992306
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H2 8.94902163375 3.11100106696 0.0129999790117
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H2 8.9909853865 -0.0100000204905 2.79399745931
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H2 6.06098409246 0.0420000013919 6.018014903
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H2 6.15602431937 3.00200114524 8.7079814146
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H2 8.92198067832 3.0690002718 5.90900439774
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H2 8.98802199413 0.132000079971 9.00601401927
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H2 5.91598953692 0.156999998903 11.9360153133
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H2 6.01097684611 2.8409989791 14.9089857968
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H2 8.97399879806 2.98999940612 11.9060109655
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H2 8.94600532365 -0.011999992838 14.7619803679
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H2 5.87100947407 5.8559808413 -0.118999783453
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H2 6.16401489524 8.84297452087 3.01699802737
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H2 9.19302524528 8.76201040774 0.075999901723
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H2 8.8339785083 5.96499134656 2.83499810954
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H2 5.9870051185 6.00298627024 5.94101961895
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H2 5.97700366923 8.97399879806 8.83900569179
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H2 9.02501148111 8.84599083096 6.02198373208
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H2 8.84800170436 5.69399969732 9.14301799894
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H2 5.92398011279 6.03198518135 11.8649997317
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H2 6.0190203397 8.82699336913 14.8660166074
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H2 8.834983945 9.07602416415 11.9409895791
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H2 8.89102381154 6.03902323824 14.8950155185
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H2 5.8559808413 11.9979819646 0.104999871185
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H2 5.82798736689 14.7829887031 2.90299738102
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H2 8.94198357686 14.8989843475 -0.0420000013919
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H2 8.93002417191 11.9660196611 3.01499773752
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H2 6.07299641512 11.8649997317 5.91202070784
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H2 6.03097974465 14.8909937717 8.97902598156
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H2 8.97198792467 14.8580260315 5.88302179673
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H2 8.95701220962 11.8349953839 8.96701365889
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H2 5.96599678326 11.8819863202 12.0440203819
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H2 5.94699932142 14.7049879824 14.7739926905
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H2 8.87599517877 14.852998848 11.9509910284
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H2 8.9919908232 11.9170178515 14.9289886954
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H2 11.9460167626 0.0880000533142 -0.0279999832887
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H2 11.8290156815 3.08100201092 3.11700193652
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H2 15.0040260237 3.0330003462 -0.00799999522534
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H2 14.8280216837 0.11999992838 3.0289997665
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H2 11.9060109655 0.0169999766244 5.99499569437
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H2 11.8729903076 2.91599926507 9.01601546854
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H2 14.9069749234 3.06199925731 5.96001708079
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H2 14.9479861572 -0.122000218234 8.8639828561
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H2 11.8690214785 -0.118000167703 11.9299826931
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H2 11.9319935665 2.86300216749 14.9789959417
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H2 14.8350068229 2.97599737714 12.0179848631
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H2 14.8519934113 -0.217999843432 14.7829887031
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H2 11.8919877694 5.99002142859 0.0579999389248
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H2 11.8159979221 8.68400968698 2.93600216361
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H2 14.9579876065 8.87599517877 -0.0550000333213
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H2 14.8399810886 6.06098409246 2.91599926507
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H2 11.9109852313 5.97102396676 5.72601491853
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H2 11.9209866806 8.94701076035 8.91499553915
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H2 15.0320194981 8.97198792467 5.83100367699
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H2 14.6990082799 5.88900149921 8.93097669089
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H2 11.764985239 5.84402143636 11.8460022699
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H2 11.9830062496 8.75502526857 14.9330104422
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H2 14.8399810886 8.92600242512 11.9470221993
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H2 14.9759796316 5.71199172246 14.7709763805
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H2 11.823988498 11.8709794342 -0.0070000090516
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H2 11.8939986428 14.8399810886 2.77099941776
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H2 15.0390046373 14.9279832587 0.0209999742371
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H2 14.8760180566 11.8509765357 2.90999839551
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H2 11.7849881376 11.9340044399 6.07098554172
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H2 11.93702075 14.6810162548 8.92901873521
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H2 14.9350213156 14.9020006576 5.87302034746
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H2 14.8819977591 11.9440058892 9.00701945597
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H2 11.9409895791 11.9560182119 11.8770120544
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H2 11.7910207578 14.8999897842 14.9550242141
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H2 14.838023133 14.9469807205 11.8309736371
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H2 14.8909937717 12.0050200215 15.0500115233
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26
tools/i-pi/examples/tutorial/tutorial-1/tutorial-1.xml
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26
tools/i-pi/examples/tutorial/tutorial-1/tutorial-1.xml
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<simulation verbosity='high'>
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<initialize nbeads='4'>
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<file mode='pdb' units='angstrom'> our_ref.pdb </file>
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<velocities mode='thermal' units='kelvin'> 25 </velocities>
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</initialize>
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<output prefix='tut1'>
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<properties filename='md' stride='1'> [step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, potential{kelvin}, kinetic_cv{kelvin}] </properties>
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<properties filename='force' stride='20'> [atom_f{piconewton}(atom=0;bead=0)] </properties>
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<trajectory filename='pos' stride='100' format='pdb' cell_units='angstrom'> positions{angstrom} </trajectory>
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<checkpoint filename='checkpoint' stride='1000' overwrite='True'/>
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</output>
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<total_steps> 5000 </total_steps>
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<forces>
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<socket mode="inet">
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<address>localhost</address>
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<port> 31415 </port>
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</socket>
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</forces>
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<ensemble mode='nvt'>
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<thermostat mode='pile_g'>
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<tau units='femtosecond'> 25 </tau>
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</thermostat>
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<timestep units='femtosecond'> 1 </timestep>
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<temperature units='kelvin'> 25 </temperature>
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</ensemble>
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</simulation>
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Reference in New Issue
Block a user