forked from lijiext/lammps
Eliminated another initialization error and tweaked rdf-adf example
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Aidan Thompson
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8aecefe233
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8223f5e0a3
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@ -133,7 +133,7 @@ arguments are specified.
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The first ADF value for a bin is calculated from the histogram count by
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dividing by the total number of triples satisfying the criteria,
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so that the integral of the ADF w.r.t. angle is one i.e. the ADF
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so that the integral of the ADF w.r.t. angle is 1, i.e. the ADF
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is a probability density function.
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The second ADF value is reported as a cumulative sum of
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@ -147,9 +147,15 @@ number radial distribution function.
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The {ordinate} optional keyword determines
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whether the bins are of uniform angular size from zero
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to 180 ({degree}), zero to Pi ({radian}), or the
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cosine of the angle uniform in the range \[-1,1\] ({cosine}).
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Regardless of which is chosen, the first ADF will be normalized
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so that the integral w.r.t. the ordinate is one.
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cosine of the angle uniform in the range \[-1,1\] ({cosine}).
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{cosine} has the advantage of eliminating the {acos()} function
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call, which speeds up the compute by 2-3x, and it is also preferred
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on physical grounds, because the for uniformly distributed particles
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in 3D, the angular probability density w.r.t dtheta is
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sin(theta)/2, while for d(cos(theta)), it is 1/2,
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Regardless of which ordinate is chosen, the first column of ADF
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values is normalized w.r.t. the range of that ordinate, so that
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the integral is 1.
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The simplest way to output the results of the compute adf calculation
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to a file is to use the "fix ave/time"_fix_ave_time.html command, for
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@ -177,7 +183,7 @@ the angle in degrees or radians, or the cosine of the angle. Each
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subsequent pair of columns gives the first and second kinds of ADF
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for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values
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in the first ADF column are normalized numbers >= 0.0,
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whose integral w.r.t. the ordinate is one,
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whose integral w.r.t. the ordinate is 1,
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i.e. the first ADF is a normalized probability distribution.
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The values in the second ADF column are also numbers >= 0.0.
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They are the cumulative density distribution of angles per atom.
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@ -1,3 +1,5 @@
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# Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom)
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units real
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atom_style full
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@ -35,8 +37,8 @@ run 500
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reset_timestep 0
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compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
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compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 &
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1 2 1 0.0 1.2 1.5 2.5
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compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 &
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2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O
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fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
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fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector
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@ -2,48 +2,48 @@
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# TimeStep Number-of-rows
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# Row c_gofa[1] c_gofa[2] c_gofa[3] c_gofa[4] c_gofa[5]
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1000 45
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1 2 0 0 0.570997 4.0364e-06
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2 6 0 0 1.34922 1.33246e-05
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3 10 0 0 0.844388 1.94267e-05
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4 14 0 0 0.476996 2.34028e-05
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5 18 0 0 0.161187 2.46115e-05
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6 22 0 0 0.0477465 2.47703e-05
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7 26 0 0 0.00511569 2.48353e-05
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8 30 0 0 0 2.48353e-05
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9 34 0 0 0 2.48353e-05
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10 38 0 0 0.0179049 2.497e-05
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11 42 0.00139303 0.00112 0 2.497e-05
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12 46 0.0970866 0.0791067 0 2.497e-05
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13 50 0.421047 0.417227 0 2.497e-05
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14 54 0.503109 0.821333 0 2.497e-05
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15 58 0.403317 1.14533 0 2.497e-05
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16 62 0.384523 1.45431 0 2.497e-05
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17 66 0.425895 1.79643 0 2.497e-05
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18 70 0.494575 2.1937 0 2.497e-05
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19 74 0.547429 2.63327 0.00716197 2.50218e-05
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20 78 0.584521 3.10253 0.0119366 2.51428e-05
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21 82 0.612285 3.59409 0.0966866 2.56506e-05
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22 86 0.643119 4.1105 0.0868815 2.64003e-05
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23 90 0.669958 4.64829 0.245468 2.77959e-05
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24 94 0.685175 5.19837 0.318537 3.01911e-05
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25 98 0.68985 5.75207 0.608171 3.48379e-05
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26 102 0.681411 6.29909 0.825076 4.16049e-05
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27 106 0.660197 6.82903 1.2987 5.06221e-05
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28 110 0.644879 7.34685 1.58753 6.12867e-05
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29 114 0.613281 7.83923 1.1185 6.98041e-05
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30 118 0.572272 8.29867 0.961282 7.65158e-05
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31 122 0.534702 8.72795 0.546058 8.08946e-05
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32 126 0.496697 9.12669 0.64867 8.51981e-05
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33 130 0.453138 9.49045 0.518561 8.86029e-05
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34 134 0.41004 9.81964 0.561575 9.23251e-05
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35 138 0.36701 10.1143 0.355285 9.51805e-05
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36 142 0.328717 10.3782 0.297648 9.74977e-05
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37 146 0.294236 10.6145 0.0749449 9.81639e-05
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38 150 0.261134 10.8242 0.0856879 9.87562e-05
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39 154 0.223727 11.0039 0.0537574 9.9216e-05
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40 158 0.19037 11.1567 0.0827037 9.95624e-05
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41 162 0.156173 11.2822 0.0149208 9.97358e-05
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42 166 0.119999 11.3785 0.00895247 9.98317e-05
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43 170 0.0853136 11.447 0.00596831 9.98799e-05
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44 174 0.0502058 11.4873 0 9.98799e-05
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45 178 0.0171616 11.5011 0 9.98799e-05
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1 2 0 0 0 0
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2 6 0 0 0 0
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3 10 0 0 0 0
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4 14 0 0 0 0
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5 18 0 0 0 0
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6 22 0 0 0 0
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7 26 0 0 0 0
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8 30 0 0 0 0
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9 34 0 0 0 0
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10 38 0 0 0 0
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11 42 0.00152868 0.00123333 0 0
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12 46 0.096401 0.07888 0 0
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13 50 0.418453 0.41588 0 0
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14 54 0.506477 0.82378 0 0
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15 58 0.408265 1.15264 0 0
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16 62 0.39048 1.46717 0 0
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17 66 0.43199 1.81511 0 0
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18 70 0.495001 2.21377 0 0
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19 74 0.549314 2.65613 0 0
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20 78 0.586929 3.12873 0.000290833 2e-05
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21 82 0.619347 3.62739 0.00150483 0.000123333
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22 86 0.644793 4.14651 0.00573476 0.000516667
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23 90 0.664615 4.68151 0.00996515 0.0012
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24 94 0.680251 5.22921 0.0147164 0.00221
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25 98 0.679622 5.77635 0.0195919 0.00355333
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26 102 0.675331 6.32011 0.0279862 0.00547333
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27 106 0.659266 6.85083 0.0431972 0.00843667
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28 110 0.640721 7.36672 0.0679453 0.0130967
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29 114 0.609075 7.85709 0.0903345 0.0192933
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30 118 0.578386 8.32278 0.12826 0.0280933
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31 122 0.535658 8.75409 0.169594 0.0397267
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32 126 0.494864 9.15256 0.208251 0.05401
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33 130 0.4498 9.51475 0.275366 0.0728967
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34 134 0.40817 9.8434 0.354045 0.09718
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35 138 0.362856 10.1356 0.459385 0.12869
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36 142 0.328968 10.4005 0.606056 0.170257
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37 146 0.291793 10.6354 0.796038 0.224857
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38 150 0.259831 10.8446 1.04618 0.296613
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39 154 0.2281 11.0283 1.34162 0.38863
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40 158 0.191749 11.1827 1.62681 0.500213
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41 162 0.15663 11.3088 1.86309 0.627997
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42 166 0.121865 11.407 1.89445 0.757927
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43 170 0.0881334 11.4779 1.67713 0.872957
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44 174 0.0523029 11.52 1.17909 0.953827
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45 178 0.0169789 11.5337 0.417313 0.98245
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@ -384,7 +384,7 @@ void ComputeADF::compute_array()
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// zero the central atom counts
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for (i = 0; i < ntriples; i++)
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iatomcount[m] = 0;
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iatomcount[i] = 0;
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// tally the ADFs
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// all three atoms i, j, and k must be in fix group
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