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Update variable.rst documentation

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Sachith Dunatunga
2024-12-21 11:16:01 -08:00
parent 8c6a1f01f5
commit af4a731ef2
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doc/src/variable.rst
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@ -56,7 +56,7 @@ Syntax
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z),
ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x)
group functions = count(group), mass(group), charge(group),
xcm(group,dim), vcm(group,dim), fcm(group,dim),
bound(group,dir), gyration(group), ke(group),
@ -532,37 +532,37 @@ functions, special functions, feature functions, atom values, atom
vectors, custom atom properties, compute references, fix references, and references to other
variables.
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Number | 0.2, 100, 1.0e20, -15.4, etc |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Constant | PI, version, on, off, true, false, yes, no |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Thermo keywords | vol, pe, ebond, etc |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math operators | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Group functions | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout() |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Custom atom properties | i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Other variables | v_name, v_name[i] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Number | 0.2, 100, 1.0e20, -15.4, etc |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Constant | PI, version, on, off, true, false, yes, no |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Thermo keywords | vol, pe, ebond, etc |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math operators | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x) |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Group functions | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout() |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Custom atom properties | i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j] |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Other variables | v_name, v_name[i] |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
Most of the formula elements produce a scalar value. Some produce a
global or per-atom vector of values. Global vectors can be produced
@ -860,6 +860,9 @@ run, according to one of these formulas, where omega = 2 PI / period:
where dt = the timestep size.
The sign(x) function returns 1.0 if the value is greater than or equal
to 0.0, and -1.0 otherwise.
The run begins on startstep. Startstep can span multiple runs, using
the *start* keyword of the :doc:`run <run>` command. See the :doc:`run
<run>` command for details of how to do this. Note that the