Hello,
My box size is 100 angstrom. When I am calculate the RDF of all atoms by using
compute myRDFall_1 all rdf 200
The G® is plotted till r = 80 angstrom.
But, when I am calculate the RDF for a particular type of atoms,
compute myRDFall_1 all rdf 200 1 1
The G® is plotted till r = 2 angstrom.
Kindly let me know how to get both these RDFs for an equal r value.
Please review the concept of minimum image convention. What you are asking makes no sense from a simulation perspective.
Best,
Dylan
Please review the concept of minimum image convention. What you are asking makes no sense from a simulation perspective.
Please note, that the MD implementation of LAMMPS is not subject to minimum image conventions.
LAMMPS creates real copies of local atoms around the individual subdomains from the neighboring subdomains, so cutoffs are in general not limited to half the box length, but by the communication cutoff (and available memory).
axel.
Hello,
My box size is 100 angstrom. When I am calculate the RDF of all atoms by usingcompute myRDFall_1 all rdf 200
The G(r) is plotted till r = 80 angstrom.But, when I am calculate the RDF for a particular type of atoms,
compute myRDFall_1 all rdf 200 1 1
The G(r) is plotted till r = 2 angstrom.Kindly let me know how to get both these RDFs for an equal r value.
impossible to say without seeing the rest of your input and knowing the LAMMPS version and platform, that you are using.
axel.
Thanks for your responses Dr. Kohlmeyer and Dr. Dylan.
Lammps version is- 16 March 2018.
I am attaching the input below. I would request you to take a quick look. There are 5 metals in my system and I am trying to calculate the RDF between all like pairs and unlike pairs.
units metal
dimension 3
boundary p p p
atom_style atomic
variable latparam equal 3.21
lattice bcc {latparam}
region whole block 0 31.5 0 31.5 0 31.5
create_box 5 whole
lattice bcc {latparam} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
create_atoms 1 region whole
variable fa equal 12080
variable fb equal 9368
variable fc equal 3098
variable fd equal 1547
variable ft equal 62559
set type 1 type/fraction 2 (v_fa/v_ft) 1734536
set type 2 type/fraction 3 (v_fb/(12080)) 1734535
set type 3 type/fraction 4 (v_fc/(9368)) 1734534
set type 4 type/fraction 5 (v_fd/(3098)) 1734533
group Mo type 1
group W type 2
group Ta type 3
group Ti type 4
group Zr type 5
pair_style eam/alloy
pair_coeff * * MoTaWTiZr.set Mo Ta W Ti Zr
min_style cg
min_modify dmax 0.1
thermo 10000
thermo_style multi
minimize 1e-15 1e-15 1000000 1000000
compute csym all centro/atom bcc
compute peratom all pe/atom
reset_timestep 0
timestep 0.001
velocity all create 4000 123456 dist gaussian
fix 123 all npt temp 4000 4000 1 iso 0 0 1 drag 1
thermo 1000
thermo_style custom step temp press ke pe etotal vol density
run 90000
compute myRDFMo_Mo all rdf 200 1 1
fix 101 Mo ave/time 100 1 100 c_myRDFMo_Mo[*] file tmp1_Mo.rdf mode vector
compute myRDFW_W all rdf 200 2 2
fix 102 W ave/time 100 1 100 c_myRDFW_W[*] file tmp1_W.rdf mode vector
compute myRDFTa_Ta all rdf 200 3 3
fix 103 Ta ave/time 100 1 100 c_myRDFTa_Ta[*] file tmp1_Ta.rdf mode vector
compute myRDFTi_Ti all rdf 200 4 4
fix 104 Ti ave/time 100 1 100 c_myRDFTi_Ti[*] file tmp1_Ti.rdf mode vector
compute myRDFZr_Zr all rdf 200 5 5
fix 105 Zr ave/time 100 1 100 c_myRDFZr_Zr[*] file tmp1_Zr.rdf mode vector
compute myRDFMo_W all rdf 200 1 2
fix 106 all ave/time 100 1 100 c_myRDFMo_W[*] file tmp1_MoW.rdf mode vector
compute myRDFMo_Ta all rdf 200 1 3
fix 107 all ave/time 100 1 100 c_myRDFMo_Ta[*] file tmp1_MoTa.rdf mode vector
compute myRDFMo_Ti all rdf 200 1 4
fix 108 all ave/time 100 1 100 c_myRDFMo_Ti[*] file tmp1_MoTi.rdf mode vector
compute myRDFMo_Zr all rdf 200 1 5
fix 109 all ave/time 100 1 100 c_myRDFMo_Zr[*] file tmp1_MoZr.rdf mode vector
compute myRDFW_Ta all rdf 200 2 3
fix 110 all ave/time 100 1 100 c_myRDFW_Ta[*] file tmp1_WTa.rdf mode vector
compute myRDFW_Ti all rdf 200 2 4
fix 111 all ave/time 100 1 100 c_myRDFW_Ti[*] file tmp1_WTi.rdf mode vector
compute myRDFW_Zr all rdf 200 2 5
fix 112 all ave/time 100 1 100 c_myRDFW_Zr[*] file tmp1_WZr.rdf mode vector
compute myRDFTa_Ti all rdf 200 3 4
fix 113 all ave/time 100 1 100 c_myRDFTa_Ti[*] file tmp1_TaTi.rdf mode vector
compute myRDFTa_Zr all rdf 200 3 5
fix 114 all ave/time 100 1 100 c_myRDFTa_Zr[*] file tmp1_TaZr.rdf mode vector
compute myRDFTi_Zr all rdf 200 4 5
fix 115 all ave/time 100 1 100 c_myRDFTi_Zr[*] file tmp1_TiZr.rdf mode vector
compute myRDFall_1 all rdf 200
fix 116 all ave/time 100 1 100 c_myRDFall_1[*] file tmp1_all.rdf mode vector
The output from the last line (rdf for all atoms) in the above code gives a radius ‘r’ ranging from 0 to >80 angstroms -
The output from all other RDF computations is similar to this figure below, with x axis range from 0 to ~2 angstroms.
My question is - is there a way to make the radius ‘r’ range same for both RDF of all atoms and RDF of specific groupwise atoms ?
you are interpreting the data in the .rdf files incorrectly.
the first column is the bin number, the second column is radius, the third column is the RDF and the fourth column is the integrated RDF (which is the number of neighboring atoms up to the value of r.
you seem to be interpreting the integrated RDF as radius.
the RDF data is in all cases computed from 0 to 7.15537, the force cutoff of your EAM potential.
if you look at your plots, they look completely unreasonable. there should be excluded volume of the atoms for at least about 2 angstrom and thus the RDF zero or near zero.
please also note, that it is not necessary, to have this many compute rdf commands, all the different computations of RDFs of type pairs can be done in a single compute RDF statement.
please have a look at the documentation again.
this is entirely a user issue. LAMMPS is working correctly and as documented.
axel.