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Merge pull request #3246 from GenieTim/compute-abs-sum

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Implement a aveabs and sumabs reduce command
This commit is contained in:
Axel Kohlmeyer
2022-05-04 14:46:54 -04:00
committed by GitHub
parent 61214b9a52 af32267db3
commit ad6cebb049
3 changed files with 20 additions and 11 deletions
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11
doc/src/compute_reduce.rst
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@ -23,7 +23,7 @@ Syntax
*reduce/region* arg = region-ID
region-ID = ID of region to use for choosing atoms
* mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq*
* mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq* or *sumabs* or *aveabs*
* one or more inputs can be listed
* input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
@ -77,7 +77,10 @@ option sums the square of the values in the vector into a global
total. The *avesq* setting does the same as *sumsq*, then divides the
sum of squares by the number of values. The last two options can be
useful for calculating the variance of some quantity, e.g. variance =
sumsq - ave\^2.
sumsq - ave\^2. The *sumabs* option sums the absolute values in the
vector into a global total. The *aveabs* setting does the same as
*sumabs*, then divides the sum of absolute values by the number of
values.
Each listed input is operated on independently. For per-atom inputs,
the group specified with this command means only atoms within the
@ -189,7 +192,7 @@ value. If multiple inputs are specified, this compute produces a
global vector of values, the length of which is equal to the number of
inputs specified.
As discussed below, for the *sum* and *sumsq* modes, the value(s)
As discussed below, for the *sum*, *sumabs* and *sumsq* modes, the value(s)
produced by this compute are all "extensive", meaning their value
scales linearly with the number of atoms involved. If normalized
values are desired, this compute can be accessed by the :doc:`thermo_style custom <thermo_style>` command with :doc:`thermo_modify norm yes <thermo_modify>` set as an option. Or it can be accessed by a
@ -208,7 +211,7 @@ compute as input. See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
All the scalar or vector values calculated by this compute are
"intensive", except when the *sum* or *sumsq* modes are used on
"intensive", except when the *sum*, *sumabs* or *sumsq* modes are used on
per-atom or local vectors, in which case the calculated values are
"extensive".

18
src/compute_reduce.cpp
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@ -54,6 +54,8 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
mode = SUM;
else if (strcmp(arg[iarg], "sumsq") == 0)
mode = SUMSQ;
else if (strcmp(arg[iarg], "sumabs") == 0)
mode = SUMABS;
else if (strcmp(arg[iarg], "min") == 0)
mode = MINN;
else if (strcmp(arg[iarg], "max") == 0)
@ -62,6 +64,8 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
mode = AVE;
else if (strcmp(arg[iarg], "avesq") == 0)
mode = AVESQ;
else if (strcmp(arg[iarg], "aveabs") == 0)
mode = AVEABS;
else
error->all(FLERR, "Illegal compute {} operation {}", style, arg[iarg]);
iarg++;
@ -253,7 +257,7 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
if (nvalues == 1) {
scalar_flag = 1;
if (mode == SUM || mode == SUMSQ)
if (mode == SUM || mode == SUMSQ || mode == SUMABS)
extscalar = 1;
else
extscalar = 0;
@ -262,7 +266,7 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
} else {
vector_flag = 1;
size_vector = nvalues;
if (mode == SUM || mode == SUMSQ)
if (mode == SUM || mode == SUMSQ || mode == SUMABS)
extvector = 1;
else
extvector = 0;
@ -339,13 +343,13 @@ double ComputeReduce::compute_scalar()
double one = compute_one(0, -1);
if (mode == SUM || mode == SUMSQ) {
if (mode == SUM || mode == SUMSQ || mode == SUMABS) {
MPI_Allreduce(&one, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
} else if (mode == MINN) {
MPI_Allreduce(&one, &scalar, 1, MPI_DOUBLE, MPI_MIN, world);
} else if (mode == MAXX) {
MPI_Allreduce(&one, &scalar, 1, MPI_DOUBLE, MPI_MAX, world);
} else if (mode == AVE || mode == AVESQ) {
} else if (mode == AVE || mode == AVESQ || mode == AVEABS) {
MPI_Allreduce(&one, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
bigint n = count(0);
if (n) scalar /= n;
@ -366,7 +370,7 @@ void ComputeReduce::compute_vector()
indices[m] = index;
}
if (mode == SUM || mode == SUMSQ) {
if (mode == SUM || mode == SUMSQ || mode == AVEABS) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m], &vector[m], 1, MPI_DOUBLE, MPI_SUM, world);
@ -412,7 +416,7 @@ void ComputeReduce::compute_vector()
}
}
} else if (mode == AVE || mode == AVESQ) {
} else if (mode == AVE || mode == AVESQ || mode == AVEABS) {
for (int m = 0; m < nvalues; m++) {
MPI_Allreduce(&onevec[m], &vector[m], 1, MPI_DOUBLE, MPI_SUM, world);
bigint n = count(m);
@ -646,6 +650,8 @@ void ComputeReduce::combine(double &one, double two, int i)
one += two;
else if (mode == SUMSQ || mode == AVESQ)
one += two * two;
else if (mode == SUMABS || mode == AVEABS)
one += std::fabs(two);
else if (mode == MINN) {
if (two < one) {
one = two;

2
src/compute_reduce.h
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@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class ComputeReduce : public Compute {
public:
enum { SUM, SUMSQ, MINN, MAXX, AVE, AVESQ };
enum { SUM, SUMSQ, SUMABS, MINN, MAXX, AVE, AVESQ, AVEABS };
enum { PERATOM, LOCAL };
ComputeReduce(class LAMMPS *, int, char **);