Added documentation, added an example, avoided position round off, added in compute_pe's compute_scalar, now fix produces per-atom array instead of global array
This commit is contained in:
Sievers
78
doc/src/fix_num_diff.rst
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78
doc/src/fix_num_diff.rst
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.. index:: fix numdiff
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fix numdiff command
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====================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID numdiff Nevery Delta
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* numdiff = style name of this fix command
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* Nevery = calculate force by finite difference every this many timesteps
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* Delta = finite difference displacement length (distance units)
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Examples
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""""""""
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.. parsed-literal::
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fix 1 all numdiff 1 0.0001
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fix 1 all numdiff 10 1e-6
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fix 1 all numdiff 100 0.01
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Description
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"""""""""""
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Calculate forces through finite difference of energy versus position.
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The resulting per-atom forces can be used by :doc:`dump custom <dump>`.
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The group specified with the command means only atoms within the group
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have their averages computed. Results are set to 0.0 for atoms not in
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the group.
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----------
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The *Nevery*\ argument specifies on what timesteps the force will
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be used calculated by finite difference.
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The *Delta*\ argument specifies the positional displacement each
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atom will undergo.
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----------
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**Restart, fix\_modify, output, run start/stop, minimize info:**
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix. No global scalar or vector quantities are
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stored by this fix for access by various :doc:`output commands <Howto_output>`.
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This fix produces a per-atom array which can be accessed by
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various :doc:`output commands <Howto_output>`. . This fix produces
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a per-atom array of the forces calculated by finite difference. The
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per-atom values should only be accessed on timesteps that are multiples
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of *Nfreq* since that is when the finite difference forces are calculated.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`dynamical_matrix <dynamical_matrix>`,
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**Default:** none
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13
examples/numdiff/README.md
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13
examples/numdiff/README.md
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# LAMMPS FIX NUMDIFF EXAMPLE
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## Numerical Difference Fix
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This directory contains the ingredients to run an NVE simulation using the numerical difference fix and calculate error in forces.
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Example:
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```
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NP=4 #number of processors
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mpirun -np $NP lmp_mpi -in.numdiff
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```
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## Required LAMMPS packages: MOLECULE package
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886
examples/numdiff/argon.lmp
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886
examples/numdiff/argon.lmp
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LAMMPS description
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864 atoms
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0 bonds
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0 angles
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0 dihedrals
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0 impropers
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1 atom types
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0 bond types
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0 angle types
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0 dihedral types
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0 improper types
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0.0000000 32.146000 xlo xhi
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0.0000000 32.146000 ylo yhi
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0.0000000 32.146000 zlo zhi
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Atoms
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1 1 1 0.0000000 0.0000000 2.6790000 2.6790000
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2 2 1 0.0000000 0.0000000 2.6790000 8.0360000
|
||||
3 3 1 0.0000000 0.0000000 2.6790000 13.3940000
|
||||
4 4 1 0.0000000 0.0000000 2.6790000 18.7520000
|
||||
5 5 1 0.0000000 0.0000000 2.6790000 24.1090000
|
||||
6 6 1 0.0000000 0.0000000 2.6790000 29.4670000
|
||||
7 7 1 0.0000000 0.0000000 8.0360000 2.6790000
|
||||
8 8 1 0.0000000 0.0000000 8.0360000 8.0360000
|
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9 9 1 0.0000000 0.0000000 8.0360000 13.3940000
|
||||
10 10 1 0.0000000 0.0000000 8.0360000 18.7520000
|
||||
11 11 1 0.0000000 0.0000000 8.0360000 24.1090000
|
||||
12 12 1 0.0000000 0.0000000 8.0360000 29.4670000
|
||||
13 13 1 0.0000000 0.0000000 13.3940000 2.6790000
|
||||
14 14 1 0.0000000 0.0000000 13.3940000 8.0360000
|
||||
15 15 1 0.0000000 0.0000000 13.3940000 13.3940000
|
||||
16 16 1 0.0000000 0.0000000 13.3940000 18.7520000
|
||||
17 17 1 0.0000000 0.0000000 13.3940000 24.1090000
|
||||
18 18 1 0.0000000 0.0000000 13.3940000 29.4670000
|
||||
19 19 1 0.0000000 0.0000000 18.7520000 2.6790000
|
||||
20 20 1 0.0000000 0.0000000 18.7520000 8.0360000
|
||||
21 21 1 0.0000000 0.0000000 18.7520000 13.3940000
|
||||
22 22 1 0.0000000 0.0000000 18.7520000 18.7520000
|
||||
23 23 1 0.0000000 0.0000000 18.7520000 24.1090000
|
||||
24 24 1 0.0000000 0.0000000 18.7520000 29.4670000
|
||||
25 25 1 0.0000000 0.0000000 24.1090000 2.6790000
|
||||
26 26 1 0.0000000 0.0000000 24.1090000 8.0360000
|
||||
27 27 1 0.0000000 0.0000000 24.1090000 13.3940000
|
||||
28 28 1 0.0000000 0.0000000 24.1090000 18.7520000
|
||||
29 29 1 0.0000000 0.0000000 24.1090000 24.1090000
|
||||
30 30 1 0.0000000 0.0000000 24.1090000 29.4670000
|
||||
31 31 1 0.0000000 0.0000000 29.4670000 2.6790000
|
||||
32 32 1 0.0000000 0.0000000 29.4670000 8.0360000
|
||||
33 33 1 0.0000000 0.0000000 29.4670000 13.3940000
|
||||
34 34 1 0.0000000 0.0000000 29.4670000 18.7520000
|
||||
35 35 1 0.0000000 0.0000000 29.4670000 24.1090000
|
||||
36 36 1 0.0000000 0.0000000 29.4670000 29.4670000
|
||||
37 37 1 0.0000000 5.3580000 2.6790000 2.6790000
|
||||
38 38 1 0.0000000 5.3580000 2.6790000 8.0360000
|
||||
39 39 1 0.0000000 5.3580000 2.6790000 13.3940000
|
||||
40 40 1 0.0000000 5.3580000 2.6790000 18.7520000
|
||||
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|
||||
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|
||||
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|
||||
44 44 1 0.0000000 5.3580000 8.0360000 8.0360000
|
||||
45 45 1 0.0000000 5.3580000 8.0360000 13.3940000
|
||||
46 46 1 0.0000000 5.3580000 8.0360000 18.7520000
|
||||
47 47 1 0.0000000 5.3580000 8.0360000 24.1090000
|
||||
48 48 1 0.0000000 5.3580000 8.0360000 29.4670000
|
||||
49 49 1 0.0000000 5.3580000 13.3940000 2.6790000
|
||||
50 50 1 0.0000000 5.3580000 13.3940000 8.0360000
|
||||
51 51 1 0.0000000 5.3580000 13.3940000 13.3940000
|
||||
52 52 1 0.0000000 5.3580000 13.3940000 18.7520000
|
||||
53 53 1 0.0000000 5.3580000 13.3940000 24.1090000
|
||||
54 54 1 0.0000000 5.3580000 13.3940000 29.4670000
|
||||
55 55 1 0.0000000 5.3580000 18.7520000 2.6790000
|
||||
56 56 1 0.0000000 5.3580000 18.7520000 8.0360000
|
||||
57 57 1 0.0000000 5.3580000 18.7520000 13.3940000
|
||||
58 58 1 0.0000000 5.3580000 18.7520000 18.7520000
|
||||
59 59 1 0.0000000 5.3580000 18.7520000 24.1090000
|
||||
60 60 1 0.0000000 5.3580000 18.7520000 29.4670000
|
||||
61 61 1 0.0000000 5.3580000 24.1090000 2.6790000
|
||||
62 62 1 0.0000000 5.3580000 24.1090000 8.0360000
|
||||
63 63 1 0.0000000 5.3580000 24.1090000 13.3940000
|
||||
64 64 1 0.0000000 5.3580000 24.1090000 18.7520000
|
||||
65 65 1 0.0000000 5.3580000 24.1090000 24.1090000
|
||||
66 66 1 0.0000000 5.3580000 24.1090000 29.4670000
|
||||
67 67 1 0.0000000 5.3580000 29.4670000 2.6790000
|
||||
68 68 1 0.0000000 5.3580000 29.4670000 8.0360000
|
||||
69 69 1 0.0000000 5.3580000 29.4670000 13.3940000
|
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70 70 1 0.0000000 5.3580000 29.4670000 18.7520000
|
||||
71 71 1 0.0000000 5.3580000 29.4670000 24.1090000
|
||||
72 72 1 0.0000000 5.3580000 29.4670000 29.4670000
|
||||
73 73 1 0.0000000 10.7150000 2.6790000 2.6790000
|
||||
74 74 1 0.0000000 10.7150000 2.6790000 8.0360000
|
||||
75 75 1 0.0000000 10.7150000 2.6790000 13.3940000
|
||||
76 76 1 0.0000000 10.7150000 2.6790000 18.7520000
|
||||
77 77 1 0.0000000 10.7150000 2.6790000 24.1090000
|
||||
78 78 1 0.0000000 10.7150000 2.6790000 29.4670000
|
||||
79 79 1 0.0000000 10.7150000 8.0360000 2.6790000
|
||||
80 80 1 0.0000000 10.7150000 8.0360000 8.0360000
|
||||
81 81 1 0.0000000 10.7150000 8.0360000 13.3940000
|
||||
82 82 1 0.0000000 10.7150000 8.0360000 18.7520000
|
||||
83 83 1 0.0000000 10.7150000 8.0360000 24.1090000
|
||||
84 84 1 0.0000000 10.7150000 8.0360000 29.4670000
|
||||
85 85 1 0.0000000 10.7150000 13.3940000 2.6790000
|
||||
86 86 1 0.0000000 10.7150000 13.3940000 8.0360000
|
||||
87 87 1 0.0000000 10.7150000 13.3940000 13.3940000
|
||||
88 88 1 0.0000000 10.7150000 13.3940000 18.7520000
|
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89 89 1 0.0000000 10.7150000 13.3940000 24.1090000
|
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90 90 1 0.0000000 10.7150000 13.3940000 29.4670000
|
||||
91 91 1 0.0000000 10.7150000 18.7520000 2.6790000
|
||||
92 92 1 0.0000000 10.7150000 18.7520000 8.0360000
|
||||
93 93 1 0.0000000 10.7150000 18.7520000 13.3940000
|
||||
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|
||||
95 95 1 0.0000000 10.7150000 18.7520000 24.1090000
|
||||
96 96 1 0.0000000 10.7150000 18.7520000 29.4670000
|
||||
97 97 1 0.0000000 10.7150000 24.1090000 2.6790000
|
||||
98 98 1 0.0000000 10.7150000 24.1090000 8.0360000
|
||||
99 99 1 0.0000000 10.7150000 24.1090000 13.3940000
|
||||
100 100 1 0.0000000 10.7150000 24.1090000 18.7520000
|
||||
101 101 1 0.0000000 10.7150000 24.1090000 24.1090000
|
||||
102 102 1 0.0000000 10.7150000 24.1090000 29.4670000
|
||||
103 103 1 0.0000000 10.7150000 29.4670000 2.6790000
|
||||
104 104 1 0.0000000 10.7150000 29.4670000 8.0360000
|
||||
105 105 1 0.0000000 10.7150000 29.4670000 13.3940000
|
||||
106 106 1 0.0000000 10.7150000 29.4670000 18.7520000
|
||||
107 107 1 0.0000000 10.7150000 29.4670000 24.1090000
|
||||
108 108 1 0.0000000 10.7150000 29.4670000 29.4670000
|
||||
109 109 1 0.0000000 16.0730000 2.6790000 2.6790000
|
||||
110 110 1 0.0000000 16.0730000 2.6790000 8.0360000
|
||||
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|
||||
112 112 1 0.0000000 16.0730000 2.6790000 18.7520000
|
||||
113 113 1 0.0000000 16.0730000 2.6790000 24.1090000
|
||||
114 114 1 0.0000000 16.0730000 2.6790000 29.4670000
|
||||
115 115 1 0.0000000 16.0730000 8.0360000 2.6790000
|
||||
116 116 1 0.0000000 16.0730000 8.0360000 8.0360000
|
||||
117 117 1 0.0000000 16.0730000 8.0360000 13.3940000
|
||||
118 118 1 0.0000000 16.0730000 8.0360000 18.7520000
|
||||
119 119 1 0.0000000 16.0730000 8.0360000 24.1090000
|
||||
120 120 1 0.0000000 16.0730000 8.0360000 29.4670000
|
||||
121 121 1 0.0000000 16.0730000 13.3940000 2.6790000
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
149 149 1 0.0000000 21.4310000 2.6790000 24.1090000
|
||||
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|
||||
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|
||||
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|
||||
153 153 1 0.0000000 21.4310000 8.0360000 13.3940000
|
||||
154 154 1 0.0000000 21.4310000 8.0360000 18.7520000
|
||||
155 155 1 0.0000000 21.4310000 8.0360000 24.1090000
|
||||
156 156 1 0.0000000 21.4310000 8.0360000 29.4670000
|
||||
157 157 1 0.0000000 21.4310000 13.3940000 2.6790000
|
||||
158 158 1 0.0000000 21.4310000 13.3940000 8.0360000
|
||||
159 159 1 0.0000000 21.4310000 13.3940000 13.3940000
|
||||
160 160 1 0.0000000 21.4310000 13.3940000 18.7520000
|
||||
161 161 1 0.0000000 21.4310000 13.3940000 24.1090000
|
||||
162 162 1 0.0000000 21.4310000 13.3940000 29.4670000
|
||||
163 163 1 0.0000000 21.4310000 18.7520000 2.6790000
|
||||
164 164 1 0.0000000 21.4310000 18.7520000 8.0360000
|
||||
165 165 1 0.0000000 21.4310000 18.7520000 13.3940000
|
||||
166 166 1 0.0000000 21.4310000 18.7520000 18.7520000
|
||||
167 167 1 0.0000000 21.4310000 18.7520000 24.1090000
|
||||
168 168 1 0.0000000 21.4310000 18.7520000 29.4670000
|
||||
169 169 1 0.0000000 21.4310000 24.1090000 2.6790000
|
||||
170 170 1 0.0000000 21.4310000 24.1090000 8.0360000
|
||||
171 171 1 0.0000000 21.4310000 24.1090000 13.3940000
|
||||
172 172 1 0.0000000 21.4310000 24.1090000 18.7520000
|
||||
173 173 1 0.0000000 21.4310000 24.1090000 24.1090000
|
||||
174 174 1 0.0000000 21.4310000 24.1090000 29.4670000
|
||||
175 175 1 0.0000000 21.4310000 29.4670000 2.6790000
|
||||
176 176 1 0.0000000 21.4310000 29.4670000 8.0360000
|
||||
177 177 1 0.0000000 21.4310000 29.4670000 13.3940000
|
||||
178 178 1 0.0000000 21.4310000 29.4670000 18.7520000
|
||||
179 179 1 0.0000000 21.4310000 29.4670000 24.1090000
|
||||
180 180 1 0.0000000 21.4310000 29.4670000 29.4670000
|
||||
181 181 1 0.0000000 26.7880000 2.6790000 2.6790000
|
||||
182 182 1 0.0000000 26.7880000 2.6790000 8.0360000
|
||||
183 183 1 0.0000000 26.7880000 2.6790000 13.3940000
|
||||
184 184 1 0.0000000 26.7880000 2.6790000 18.7520000
|
||||
185 185 1 0.0000000 26.7880000 2.6790000 24.1090000
|
||||
186 186 1 0.0000000 26.7880000 2.6790000 29.4670000
|
||||
187 187 1 0.0000000 26.7880000 8.0360000 2.6790000
|
||||
188 188 1 0.0000000 26.7880000 8.0360000 8.0360000
|
||||
189 189 1 0.0000000 26.7880000 8.0360000 13.3940000
|
||||
190 190 1 0.0000000 26.7880000 8.0360000 18.7520000
|
||||
191 191 1 0.0000000 26.7880000 8.0360000 24.1090000
|
||||
192 192 1 0.0000000 26.7880000 8.0360000 29.4670000
|
||||
193 193 1 0.0000000 26.7880000 13.3940000 2.6790000
|
||||
194 194 1 0.0000000 26.7880000 13.3940000 8.0360000
|
||||
195 195 1 0.0000000 26.7880000 13.3940000 13.3940000
|
||||
196 196 1 0.0000000 26.7880000 13.3940000 18.7520000
|
||||
197 197 1 0.0000000 26.7880000 13.3940000 24.1090000
|
||||
198 198 1 0.0000000 26.7880000 13.3940000 29.4670000
|
||||
199 199 1 0.0000000 26.7880000 18.7520000 2.6790000
|
||||
200 200 1 0.0000000 26.7880000 18.7520000 8.0360000
|
||||
201 201 1 0.0000000 26.7880000 18.7520000 13.3940000
|
||||
202 202 1 0.0000000 26.7880000 18.7520000 18.7520000
|
||||
203 203 1 0.0000000 26.7880000 18.7520000 24.1090000
|
||||
204 204 1 0.0000000 26.7880000 18.7520000 29.4670000
|
||||
205 205 1 0.0000000 26.7880000 24.1090000 2.6790000
|
||||
206 206 1 0.0000000 26.7880000 24.1090000 8.0360000
|
||||
207 207 1 0.0000000 26.7880000 24.1090000 13.3940000
|
||||
208 208 1 0.0000000 26.7880000 24.1090000 18.7520000
|
||||
209 209 1 0.0000000 26.7880000 24.1090000 24.1090000
|
||||
210 210 1 0.0000000 26.7880000 24.1090000 29.4670000
|
||||
211 211 1 0.0000000 26.7880000 29.4670000 2.6790000
|
||||
212 212 1 0.0000000 26.7880000 29.4670000 8.0360000
|
||||
213 213 1 0.0000000 26.7880000 29.4670000 13.3940000
|
||||
214 214 1 0.0000000 26.7880000 29.4670000 18.7520000
|
||||
215 215 1 0.0000000 26.7880000 29.4670000 24.1090000
|
||||
216 216 1 0.0000000 26.7880000 29.4670000 29.4670000
|
||||
217 217 1 0.0000000 2.6790000 5.3580000 2.6790000
|
||||
218 218 1 0.0000000 2.6790000 5.3580000 8.0360000
|
||||
219 219 1 0.0000000 2.6790000 5.3580000 13.3940000
|
||||
220 220 1 0.0000000 2.6790000 5.3580000 18.7520000
|
||||
221 221 1 0.0000000 2.6790000 5.3580000 24.1090000
|
||||
222 222 1 0.0000000 2.6790000 5.3580000 29.4670000
|
||||
223 223 1 0.0000000 2.6790000 10.7150000 2.6790000
|
||||
224 224 1 0.0000000 2.6790000 10.7150000 8.0360000
|
||||
225 225 1 0.0000000 2.6790000 10.7150000 13.3940000
|
||||
226 226 1 0.0000000 2.6790000 10.7150000 18.7520000
|
||||
227 227 1 0.0000000 2.6790000 10.7150000 24.1090000
|
||||
228 228 1 0.0000000 2.6790000 10.7150000 29.4670000
|
||||
229 229 1 0.0000000 2.6790000 16.0730000 2.6790000
|
||||
230 230 1 0.0000000 2.6790000 16.0730000 8.0360000
|
||||
231 231 1 0.0000000 2.6790000 16.0730000 13.3940000
|
||||
232 232 1 0.0000000 2.6790000 16.0730000 18.7520000
|
||||
233 233 1 0.0000000 2.6790000 16.0730000 24.1090000
|
||||
234 234 1 0.0000000 2.6790000 16.0730000 29.4670000
|
||||
235 235 1 0.0000000 2.6790000 21.4310000 2.6790000
|
||||
236 236 1 0.0000000 2.6790000 21.4310000 8.0360000
|
||||
237 237 1 0.0000000 2.6790000 21.4310000 13.3940000
|
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|
||||
831 831 1 0.0000000 26.7880000 5.3580000 16.0730000
|
||||
832 832 1 0.0000000 26.7880000 5.3580000 21.4310000
|
||||
833 833 1 0.0000000 26.7880000 5.3580000 26.7880000
|
||||
834 834 1 0.0000000 26.7880000 5.3580000 32.1460000
|
||||
835 835 1 0.0000000 26.7880000 10.7150000 5.3580000
|
||||
836 836 1 0.0000000 26.7880000 10.7150000 10.7150000
|
||||
837 837 1 0.0000000 26.7880000 10.7150000 16.0730000
|
||||
838 838 1 0.0000000 26.7880000 10.7150000 21.4310000
|
||||
839 839 1 0.0000000 26.7880000 10.7150000 26.7880000
|
||||
840 840 1 0.0000000 26.7880000 10.7150000 32.1460000
|
||||
841 841 1 0.0000000 26.7880000 16.0730000 5.3580000
|
||||
842 842 1 0.0000000 26.7880000 16.0730000 10.7150000
|
||||
843 843 1 0.0000000 26.7880000 16.0730000 16.0730000
|
||||
844 844 1 0.0000000 26.7880000 16.0730000 21.4310000
|
||||
845 845 1 0.0000000 26.7880000 16.0730000 26.7880000
|
||||
846 846 1 0.0000000 26.7880000 16.0730000 32.1460000
|
||||
847 847 1 0.0000000 26.7880000 21.4310000 5.3580000
|
||||
848 848 1 0.0000000 26.7880000 21.4310000 10.7150000
|
||||
849 849 1 0.0000000 26.7880000 21.4310000 16.0730000
|
||||
850 850 1 0.0000000 26.7880000 21.4310000 21.4310000
|
||||
851 851 1 0.0000000 26.7880000 21.4310000 26.7880000
|
||||
852 852 1 0.0000000 26.7880000 21.4310000 32.1460000
|
||||
853 853 1 0.0000000 26.7880000 26.7880000 5.3580000
|
||||
854 854 1 0.0000000 26.7880000 26.7880000 10.7150000
|
||||
855 855 1 0.0000000 26.7880000 26.7880000 16.0730000
|
||||
856 856 1 0.0000000 26.7880000 26.7880000 21.4310000
|
||||
857 857 1 0.0000000 26.7880000 26.7880000 26.7880000
|
||||
858 858 1 0.0000000 26.7880000 26.7880000 32.1460000
|
||||
859 859 1 0.0000000 26.7880000 32.1460000 5.3580000
|
||||
860 860 1 0.0000000 26.7880000 32.1460000 10.7150000
|
||||
861 861 1 0.0000000 26.7880000 32.1460000 16.0730000
|
||||
862 862 1 0.0000000 26.7880000 32.1460000 21.4310000
|
||||
863 863 1 0.0000000 26.7880000 32.1460000 26.7880000
|
||||
864 864 1 0.0000000 26.7880000 32.1460000 32.1460000
|
||||
|
||||
20
examples/numdiff/ff-argon.lmp
Normal file
20
examples/numdiff/ff-argon.lmp
Normal file
@ -0,0 +1,20 @@
|
||||
#############################
|
||||
#Atoms types - mass - charge#
|
||||
#############################
|
||||
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
|
||||
|
||||
variable Ar equal 1
|
||||
|
||||
#############
|
||||
#Atom Masses#
|
||||
#############
|
||||
|
||||
mass ${Ar} 39.903
|
||||
|
||||
###########################
|
||||
#Pair Potentials - Tersoff#
|
||||
###########################
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 0.0102701 3.42
|
||||
|
||||
28
examples/numdiff/in.numdiff
Normal file
28
examples/numdiff/in.numdiff
Normal file
@ -0,0 +1,28 @@
|
||||
# Numerical difference calculation of error in forces
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
boundary p p p
|
||||
read_data argon.lmp
|
||||
|
||||
include ff-argon.lmp
|
||||
|
||||
velocity all create 10 2357 mom yes dist gaussian
|
||||
|
||||
neighbor 1 bin
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix numdiff all numdiff 200 0.0001
|
||||
fix nve all nve
|
||||
|
||||
variable errx atom fx-f_numdiff[1]
|
||||
variable erry atom fy-f_numdiff[2]
|
||||
variable errz atom fz-f_numdiff[3]
|
||||
|
||||
dump forces all custom 200 force_error.dump v_errx v_erry v_errz
|
||||
thermo 200
|
||||
run 2000
|
||||
|
||||
|
||||
@ -12,14 +12,14 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_num_diff.h"
|
||||
#include <algorithm>
|
||||
#include <mpi.h>
|
||||
#include <cstring>
|
||||
#include <cmath>
|
||||
#include "atom.h"
|
||||
#include "atom_masks.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "comm.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "region.h"
|
||||
#include "respa.h"
|
||||
@ -37,9 +37,6 @@
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "group.h"
|
||||
#include <algorithm>
|
||||
|
||||
//TODO: Add energy from potentials to single energy array and then reverse comm pack and unpack
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -49,12 +46,13 @@ using namespace FixConst;
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNumDiff::FixNumDiff(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg), groupmap(NULL), local_forces(NULL), global_forces(NULL), temp_f(NULL)
|
||||
Fix(lmp, narg, arg), numdiff_forces(NULL), temp_f(NULL), temp_x(NULL), id_pe(NULL)
|
||||
{
|
||||
respa_level_support = 1;
|
||||
ilevel_respa = 0;
|
||||
eflag = 1;
|
||||
energy = 0;
|
||||
energy = 0.0;
|
||||
size_peratom_cols = 3;
|
||||
|
||||
if (narg < 5) error->all(FLERR,"Illegal fix numdiff command");
|
||||
|
||||
@ -62,7 +60,7 @@ FixNumDiff::FixNumDiff(LAMMPS *lmp, int narg, char **arg) :
|
||||
del = force->numeric(FLERR,arg[4]);
|
||||
|
||||
if (nevery <= 0)
|
||||
error->all(FLERR,"Illegal fix ave/atom command");
|
||||
error->all(FLERR,"Illegal fix numdiff command");
|
||||
|
||||
peratom_flag = 1;
|
||||
if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
|
||||
@ -70,39 +68,45 @@ FixNumDiff::FixNumDiff(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
|
||||
else kspace_compute_flag = 0;
|
||||
|
||||
igroup = group->find(arg[1]);
|
||||
if (igroup == -1) error->all(FLERR,"Could not find numerical difference group ID");
|
||||
groupbit = group->bitmask[igroup];
|
||||
gcount = group->count(igroup);
|
||||
flen = gcount*3;
|
||||
memory->create(groupmap,atom->natoms,"total_group_map:total_group_map");
|
||||
local_forces = NULL;
|
||||
global_forces = NULL;
|
||||
array_flag = 1;
|
||||
size_array_cols = 3;
|
||||
size_array_rows = gcount;
|
||||
numdiff_forces = NULL;
|
||||
|
||||
memory->create(local_forces,gcount,3,"fix_numdiff:local_forces");
|
||||
memory->create(global_forces,gcount,3,"fix_numdiff:global_forces");
|
||||
memory->grow(temp_f, atom->natoms, 3, "fix_numdiff:temporary_forces");
|
||||
maxatom1 = 0;
|
||||
|
||||
for (bigint i = 0; i < gcount; i++)
|
||||
for (int j = 0; j < 3; j++) {
|
||||
global_forces[i][j] = 0;
|
||||
local_forces[i][j] = 0;
|
||||
}
|
||||
int n = strlen(id) + 6;
|
||||
id_pe = new char[n];
|
||||
strcpy(id_pe,id);
|
||||
strcat(id_pe,"_pe");
|
||||
|
||||
char **newarg = new char*[10];
|
||||
newarg[0] = id_pe;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "pe";
|
||||
newarg[3] = (char *) "pair";
|
||||
newarg[4] = (char *) "bond";
|
||||
newarg[5] = (char *) "angle";
|
||||
newarg[6] = (char *) "dihedral";
|
||||
newarg[7] = (char *) "improper";
|
||||
newarg[8] = (char *) "kspace";
|
||||
newarg[9] = (char *) "fix";
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
|
||||
nmax = 0;
|
||||
memory->create(numdiff_forces,atom->natoms,3,"numdiff:numdiff_force");
|
||||
force_clear(numdiff_forces);
|
||||
array_atom = numdiff_forces;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNumDiff::~FixNumDiff()
|
||||
{
|
||||
memory->destroy(groupmap);
|
||||
memory->destroy(local_forces);
|
||||
memory->destroy(global_forces);
|
||||
memory->destroy(numdiff_forces);
|
||||
memory->destroy(temp_f);
|
||||
memory->destroy(temp_x);
|
||||
|
||||
modify->delete_compute(id_pe);
|
||||
delete [] id_pe;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -124,11 +128,10 @@ void FixNumDiff::init()
|
||||
{
|
||||
// check variables
|
||||
|
||||
if (gcount == atom->natoms)
|
||||
for (bigint i=0; i<atom->natoms; i++)
|
||||
groupmap[i] = i;
|
||||
else
|
||||
create_groupmap();
|
||||
int icompute = modify->find_compute(id_pe);
|
||||
if (icompute < 0)
|
||||
error->all(FLERR,"Compute ID for fix numdiff does not exist");
|
||||
pe = modify->compute[icompute];
|
||||
|
||||
if (strstr(update->integrate_style,"respa")) {
|
||||
ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
|
||||
@ -138,13 +141,6 @@ void FixNumDiff::init()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNumDiff::min_setup(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNumDiff::post_force(int vflag)
|
||||
{
|
||||
if (update->ntimestep % nevery) return;
|
||||
@ -180,45 +176,66 @@ void FixNumDiff::calculate_forces(int vflag)
|
||||
{
|
||||
int local_idx; // local index
|
||||
bigint natoms = atom->natoms;
|
||||
bigint *gm = groupmap;
|
||||
double **f = atom->f;
|
||||
double **x = atom->x;
|
||||
double temp = 1.0 / 2 / del;
|
||||
int nlocal = atom->nlocal;
|
||||
int *mask = atom->mask;
|
||||
int flag = 0;
|
||||
int allflag = 0;
|
||||
|
||||
if (atom->nmax > maxatom1) {
|
||||
memory->destroy(numdiff_forces);
|
||||
memory->destroy(temp_f);
|
||||
memory->destroy(temp_x);
|
||||
maxatom1 = atom->nmax;
|
||||
memory->create(numdiff_forces,maxatom1,3,"numdiff:numdiff_force");
|
||||
memory->create(temp_f,maxatom1,3,"numdiff:temp_f");
|
||||
memory->create(temp_x,maxatom1,3,"numdiff:temp_x");
|
||||
array_atom = numdiff_forces;
|
||||
}
|
||||
|
||||
for (bigint i = 0; i < natoms; i++)
|
||||
for (int j = 0; j < 3; j++)
|
||||
temp_f[i][j] = f[i][j];
|
||||
|
||||
for (bigint i = 0; i < natoms; i++)
|
||||
for (int j = 0; j < 3; j++)
|
||||
temp_x[i][j] = x[i][j];
|
||||
|
||||
//initialize forces to all zeros
|
||||
nd_force_clear(local_forces);
|
||||
nd_force_clear(global_forces);
|
||||
force_clear(numdiff_forces);
|
||||
|
||||
for (bigint i=1; i<=natoms; i++){
|
||||
local_idx = atom->map(i);
|
||||
if (gm[i-1] < 0)
|
||||
continue;
|
||||
if (mask[local_idx] && groupbit) flag = 1;
|
||||
else flag = 0;
|
||||
MPI_Allreduce(&flag, &allflag,1, MPI_INT, MPI_SUM,world);
|
||||
if (!allflag) continue;
|
||||
for (int alpha=0; alpha<3; alpha++){
|
||||
displace_atom(local_idx, alpha, 1);
|
||||
update_force(vflag);
|
||||
update_energy(vflag);
|
||||
if (local_idx >= 0 && local_idx < nlocal)
|
||||
local_forces[gm[i-1]][alpha] -= energy;
|
||||
numdiff_forces[local_idx][alpha] -= energy;
|
||||
|
||||
displace_atom(local_idx,alpha,-2);
|
||||
update_force(vflag);
|
||||
update_energy(vflag);
|
||||
if (local_idx >= 0 && local_idx < nlocal) {
|
||||
local_forces[gm[i-1]][alpha] += energy;
|
||||
local_forces[gm[i-1]][alpha] *= temp;
|
||||
numdiff_forces[local_idx][alpha] += energy;
|
||||
numdiff_forces[local_idx][alpha] *= temp;
|
||||
}
|
||||
displace_atom(local_idx,alpha,1);
|
||||
}
|
||||
for (int k=0; k<gcount; k++)
|
||||
MPI_Allreduce(local_forces[k],global_forces[k],3,MPI_DOUBLE,MPI_SUM,world);
|
||||
}
|
||||
|
||||
for (bigint i = 0; i < natoms; i++)
|
||||
for (int j = 0; j < 3; j++)
|
||||
f[i][j] = temp_f[i][j];
|
||||
|
||||
for (bigint i = 0; i < natoms; i++)
|
||||
for (int j = 0; j < 3; j++)
|
||||
x[i][j] = temp_x[i][j];
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -248,9 +265,9 @@ void FixNumDiff::displace_atom(int local_idx, int direction, int magnitude)
|
||||
return negative gradient for nextra_global dof in fextra
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNumDiff::update_force(int vflag)
|
||||
void FixNumDiff::update_energy(int vflag)
|
||||
{
|
||||
force_clear();
|
||||
force_clear(atom->f);
|
||||
|
||||
if (pair_compute_flag) {
|
||||
force->pair->compute(eflag,vflag);
|
||||
@ -272,140 +289,49 @@ void FixNumDiff::update_force(int vflag)
|
||||
force->kspace->compute(eflag,vflag);
|
||||
timer->stamp(Timer::KSPACE);
|
||||
}
|
||||
// if (force->newton) {
|
||||
// comm->reverse_comm();
|
||||
// timer->stamp(Timer::COMM);
|
||||
// }
|
||||
compute_energy();
|
||||
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
clear force on own & ghost atoms
|
||||
clear other arrays as needed
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNumDiff::force_clear()
|
||||
{
|
||||
if (external_force_clear) return;
|
||||
|
||||
// clear global force array
|
||||
// if either newton flag is set, also include ghosts
|
||||
|
||||
size_t nbytes = sizeof(double) * atom->nlocal;
|
||||
if (force->newton) nbytes += sizeof(double) * atom->nghost;
|
||||
|
||||
if (nbytes) {
|
||||
memset(&atom->f[0][0],0,3*nbytes);
|
||||
}
|
||||
energy = pe->compute_scalar();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
clear forces needed
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNumDiff::nd_force_clear(double **forces)
|
||||
void FixNumDiff::force_clear(double **forces)
|
||||
{
|
||||
|
||||
size_t nbytes = sizeof(double) * flen;
|
||||
|
||||
size_t nbytes = sizeof(double) * atom->nlocal;
|
||||
if (force->newton) nbytes += sizeof(double) * atom->nghost;
|
||||
|
||||
if (nbytes) {
|
||||
memset(&forces[0][0],0,nbytes);
|
||||
memset(&forces[0][0],0,3*nbytes);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
void FixNumDiff::compute_energy()
|
||||
/* ----------------------------------------------------------------------
|
||||
pack values in local atom-based array for exchange with another proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixNumDiff::pack_exchange(int i, double *buf)
|
||||
{
|
||||
double one = 0.0;
|
||||
if (pair_compute_flag)
|
||||
one += force->pair->eng_vdwl + force->pair->eng_coul;
|
||||
|
||||
if (atom->molecular) {
|
||||
if (force->bond) one += force->bond->energy;
|
||||
if (force->angle) one += force->angle->energy;
|
||||
if (force->dihedral) one += force->dihedral->energy;
|
||||
if (force->improper) one += force->improper->energy;
|
||||
}
|
||||
|
||||
MPI_Allreduce(&one,&energy,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
if (kspace_compute_flag) energy += force->kspace->energy;
|
||||
|
||||
if (pairflag && force->pair && force->pair->tail_flag) {
|
||||
double volume = domain->xprd * domain->yprd * domain->zprd;
|
||||
energy += force->pair->etail / volume;
|
||||
}
|
||||
int n = 0;
|
||||
buf[n++] = numdiff_forces[i][0];
|
||||
buf[n++] = numdiff_forces[i][1];
|
||||
buf[n++] = numdiff_forces[i][2];
|
||||
return n;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack values in local atom-based array from exchange with another proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixNumDiff::create_groupmap()
|
||||
int FixNumDiff::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
//Create a group map which maps atom order onto group
|
||||
// groupmap[global atom index-1] = output column/row
|
||||
|
||||
int local_idx; // local index
|
||||
int gid = 0; //group index
|
||||
int nlocal = atom->nlocal;
|
||||
int *mask = atom->mask;
|
||||
bigint natoms = atom->natoms;
|
||||
int *recv = new int[comm->nprocs];
|
||||
int *displs = new int[comm->nprocs];
|
||||
bigint *temp_groupmap = new bigint[natoms];
|
||||
|
||||
//find number of local atoms in the group (final_gid)
|
||||
for (bigint i=1; i<=natoms; i++){
|
||||
local_idx = atom->map(i);
|
||||
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit)
|
||||
gid += 1; // gid at the end of loop is final_Gid
|
||||
}
|
||||
//create an array of length final_gid
|
||||
bigint *sub_groupmap = new bigint[gid];
|
||||
|
||||
gid = 0;
|
||||
//create a map between global atom id and group atom id for each proc
|
||||
for (bigint i=1; i<=natoms; i++){
|
||||
local_idx = atom->map(i);
|
||||
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit){
|
||||
sub_groupmap[gid] = i;
|
||||
gid += 1;
|
||||
}
|
||||
}
|
||||
|
||||
//populate arrays for Allgatherv
|
||||
for (int i=0; i<comm->nprocs; i++){
|
||||
recv[i] = 0;
|
||||
}
|
||||
recv[comm->me] = gid;
|
||||
MPI_Allreduce(recv,displs,comm->nprocs,MPI_INT,MPI_SUM,world);
|
||||
for (int i=0; i<comm->nprocs; i++){
|
||||
recv[i]=displs[i];
|
||||
if (i>0) displs[i] = displs[i-1]+recv[i-1];
|
||||
else displs[i] = 0;
|
||||
}
|
||||
|
||||
//combine subgroup maps into total temporary groupmap
|
||||
MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);
|
||||
std::sort(temp_groupmap,temp_groupmap+gcount);
|
||||
|
||||
//populate member groupmap based on temp groupmap
|
||||
bigint j = 0;
|
||||
for (bigint i=1; i<=natoms; i++){
|
||||
// flag groupmap contents that are in temp_groupmap
|
||||
if (j < gcount && i == temp_groupmap[j])
|
||||
groupmap[i-1] = j++;
|
||||
else
|
||||
groupmap[i-1] = -1;
|
||||
}
|
||||
|
||||
//free that memory!
|
||||
delete[] recv;
|
||||
delete[] displs;
|
||||
delete[] sub_groupmap;
|
||||
delete[] temp_groupmap;
|
||||
int n = 0;
|
||||
numdiff_forces[nlocal][0] = buf[n++];
|
||||
numdiff_forces[nlocal][1] = buf[n++];
|
||||
numdiff_forces[nlocal][2] = buf[n++];
|
||||
return n;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -414,7 +340,7 @@ void FixNumDiff::create_groupmap()
|
||||
|
||||
double FixNumDiff::compute_array(int i, int j)
|
||||
{
|
||||
return global_forces[i][j];
|
||||
return numdiff_forces[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -424,8 +350,6 @@ double FixNumDiff::compute_array(int i, int j)
|
||||
double FixNumDiff::memory_usage()
|
||||
{
|
||||
bigint bytes = 0.0;
|
||||
bytes += atom->natoms * 3 * sizeof(double); // temp_f
|
||||
bytes += 2 * flen * sizeof(double); // local_f, global_f
|
||||
bytes += gcount * sizeof(bigint); // groupmap
|
||||
bytes += 3 * atom->natoms * 3 * sizeof(double); // temp_f, temp_x, numdiff_f
|
||||
return bytes;
|
||||
}
|
||||
|
||||
@ -30,12 +30,13 @@ class FixNumDiff : public Fix {
|
||||
~FixNumDiff();
|
||||
int setmask();
|
||||
void init();
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void min_post_force(int);
|
||||
double compute_array(int, int);
|
||||
double memory_usage();
|
||||
int pack_exchange(int i, double *buf);
|
||||
int unpack_exchange(int nlocal, double *buf);
|
||||
|
||||
protected:
|
||||
int eflag; // flags for energy/virial computation
|
||||
@ -47,17 +48,15 @@ protected:
|
||||
int pair_compute_flag; // 0 if pair->compute is skipped
|
||||
int kspace_compute_flag; // 0 if kspace->compute is skipped
|
||||
|
||||
double **local_forces; // local forces from numerical difference (this might be usefull for debugging)
|
||||
double **global_forces; // global forces from numerical difference
|
||||
double **numdiff_forces; // local forces from numerical difference (this might be usefull for debugging)
|
||||
|
||||
void update_force(int vflag);
|
||||
void force_clear();
|
||||
void update_energy(int vflag);
|
||||
void force_clear(double **forces);
|
||||
// virtual void openfile(const char* filename);
|
||||
|
||||
private:
|
||||
void create_groupmap();
|
||||
void displace_atom(int local_idx, int direction, int magnitude);
|
||||
void nd_force_clear(double **forces);
|
||||
void calculate_forces(int vflag);
|
||||
void compute_energy();
|
||||
|
||||
@ -65,14 +64,15 @@ protected:
|
||||
double del;
|
||||
int nmax;
|
||||
|
||||
int igroup,groupbit;
|
||||
bigint gcount; // number of atoms in group
|
||||
bigint flen; // rank of dynamical matrix
|
||||
int scaleflag;
|
||||
int me;
|
||||
bigint *groupmap;
|
||||
double **temp_f;
|
||||
double **temp_x;
|
||||
double energy;
|
||||
int maxatom1;
|
||||
|
||||
char *id_pe;
|
||||
class Compute *pe;
|
||||
|
||||
};
|
||||
|
||||
|
||||
Reference in New Issue
Block a user