Tag: LAMMPS

Dear LAMMPS users, I am constructing a model in LAMMPS using two approaches: (1) I create a supercell and then remove atoms from specific regions to form the final model, and (2) I directly construct the model and then fill it with unit cells. I am unable to explain why…

owala February 9, 2024, 4:48pm 1 Hi all! I am hoping to simulate variable stiffness particles using the GRANULAR package. For example, I am simulating 5 grains, each of which should have a different stiffness. I am using a Hookean pair_style. I understand that I can define a spring stiffness…

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Dear community of LAMMPS users I am simulating a complex system consisting of a biomolecule (1876 atoms), a nantube of an oxide (4200 atoms) and a box of water (30000 atoms) and I get the following error: ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_half_bin_newton.cpp:156) I am…

luowh35 January 20, 2024, 10:00am 1 hello, everyone:I am reading the fix evaporate command in lammps doc.This command remove M atoms from the simulation every N steps, but there is no information for the energy.my question is: if this fix delete the M atoms, does the (potential) energy from these…

Dear developers and user, I’m running the simulation using an unmodified LAMMPS (2 Aug 2023) version. I want to use multiple GPUs and CUDA API to accelerate the PPPM alogrithm. However, I can’t access more than one GPU when running program. I have tried numerous ways to solve this problem,…

Hi, I’d like to divide my simulation box into smaller boxes (regions).Specifically, I want to have 24 smaller boxes on each axis (24x24x24). In the region command, apart from defining the boundaries of each region separately, is there any faster way to divide the cell into 24 regions on each…

I’m busy with a research project in materials science and I’m using LAMMPS for my simulations. My goal is to find the energy required for an atom to bind to the 111 surface of an fcc metal surface. I’ve successfully achieved this using periodic boundary conditions, but I need to…

In your input script you need to define the atomic coordinates, box dimensions, and atom type. For instance, to create a cubic box with a side length of 10 angstroms, you can use the following: # Set atom type and properties atom_style atomic atom_modify map array sort 0 0 #…

hello every body i have some questions a bout atomsk (windows version) . is it possible to generate a solvation box involve water and heavy matal ions using atomsk ? if the answer is yes can you tell me with what command i can generate this solvation box in windows…

Tejasva December 29, 2023, 11:35am 1 #Use Tersoff potentialpair_style tersoffpair_coeff * * SiO.tersoff Si O Si In the above command in LAMMPS, it says 3rd element in LAMMPS is mapping to Si in the tersoff file but the tersoff file contains Si Si O , Si O, Si as attached…

srz1994 December 29, 2023, 1:46pm 1 Dear LAMMPS users, I am attempting to utilize the harmonic bond potential in LAMMPS. I’m a bit confused about the meaning of the statement in the LAMMPS manual: “Note that the usual 1/2 factor is included in K.” The formula provided in the documentation…

Hi, In the computes group/group and pe/atom, is the pair keyword equal to the thermo_style keywords : evdwl + ecoul + elong, and the kspace keyword is elong? Thanks,Frank If the group/group and pe/atom group-ID is given as “all”, the values should be the same? That depends on the individual…

Sean December 20, 2023, 2:33am 1 Hello, I recently built a system with moltemplate, and I noticed a discrepancy between the number of dihedrals that the LAMMPS Data file says are present and the number of dihedrals that should be present based on my calculations, which was merely counting the…

Hi all, I am trying to use fix bond/react to simulate the polymerization process with monomers floating between two functionalized rough walls. The interaction between the wall particles is excluded and the interaction between the wall and monomers are described with lj/cut 1 1 2.5. The boundary condition is p…

I am writing a custom potential for a molecule so I want to sort all the atoms in amolecule according to their Atom ids .Any idea how that can be done ? Do you mean you already have the LAMMPS data file and you want to sort the atoms of…

ntiwari December 18, 2023, 4:18pm 1 Hi Everyone, I’m simulating a system of toy surfactants which form micelles in an electric double layer (EDL). The simulation is 2D periodic and charged, so kspace_modify slab is used. At the bottom of the box is a charged wall. At the top is…

shiwenC December 18, 2023, 1:05pm 1 hello guys, I would like to run a simulation of ideal gas for presentation of a Carnot Cycle. For an ideal gas, the potential energy is zero as there is no particle-particle interaction.Is it appropriate to set the pair style none? shiwenC December 18,…

Dear All, I have a linear coarse-grained polymer system, with nonbonded, bond, angle, and dihedral interactions as a tabulated potential. My simulations consist of 1000 polymer chains, each chain has 200 monomers. The simulations sometimes crash because of dihedral atom missing errors in some processors. I am running the latest…

m.adibi December 18, 2023, 9:39am 1 Greetings, I am trying to define a lammps input script that gets a list of forcefield files and for each forcefield file it runs simulations in multiple temperatures. One way to do this is to make an outer Uloop for force field files and…

in lammps/examples/template/h2o-co2.data: […] Angle Coeffs # harmonic1 100 109.472 100 180 […] it makes sense that the harmonic angle_coef for CO2 is 180, but why is the H2O angle 109.47 not 104.45 degrees ? what am i missing here ?? also how are the K=100 harmonic angle coefficients derived or…

Recently, I studied a system with a granular monolayer. The container is vibrated in the x direction by using the “fix wall/gran/region” command. Although the gravity exists in the system, it should be balanced with the normal force given by the botton wall. The simulation shows that the granules will…

m.adibi December 16, 2023, 6:30am 1 Greetings, I am trying to calculate the free energy of complex crystals where there are two types of atoms. I know that fix ti/spring can be used to find the free energy of simple crystals with only a single atom type. Now I was…

Dear LAMMPS users, I am trying to create Silicon Oxide (Si02) structure in LAMMPS but I am encountering some difficulties. Could anyone please help on how to accomplish that using “lattice” command or any other appropriate command in LAMMPS? I can also be directed to anywhere where similar problem has…

Hello everyone,I have implemented my own pair_style, which is non-reciprocal and long ranged. For instance: for my use case, a single particle on an average has around 80 neighbors in the high density limit. I am looking to study systems having 1000-10000 particles. In this case, would it be advantageous…

srtee December 15, 2023, 8:24am 1 I will sketch some topic templates to help users include all the necessary information when asking for help. Currently I am thinking of the following categories: results-help: when a LAMMPS simulation runs successfully (or is user-terminated) but does not give the “correct results”. Template…

I am trying to simuate ring polymers in lammps. I want to put constraint on its area by associating a potential energy porpotional to its area .The area can be calculated from all its positions of beads if provided in a serial manner .I am trying it by creating a…

I want to use langevin barostat and thermostat.So based on the documentation I am using the following line in my input script:fix 1 H2O press/langevin z 1 1 800 temp 300 300 100 dilate partial However I am getting the following error:ERROR: Unrecognized fix style ‘press/langevin’ (…/modify.cpp:917) regardssundaram The online…

I have installed LAMMPS 02Aug 2023 version and now from the bench directory I am running the test cases. I loaded the environmental modules and the path where lmp_nompi is oocated, but it ended up with following: /apps/lammps-2Aug2023/02082023/bench$ mpirun -np 4 /apps/lammps-2Aug2023/02082023/bin/lmp_mpi -in in.rhodo /apps/lammps-2Aug2023/02082023/bin/lmp_mpi: error while loading shared libraries:…

I use dump mydmp all custom 1000 dump.md.lammpstrj id type x y z fx fy fz To get a dump file that looks like ITEM: TIMESTEP 0 ITEM: NUMBER OF ATOMS 1150 ITEM: BOX BOUNDS pp pp pp -2.0000000000000000e+01 2.0000000000000000e+01 -2.0000000000000000e+01 2.0000000000000000e+01 -2.0000000000000000e+01 2.0000000000000000e+01 ITEM: ATOMS id type x y…

Hello lammps users, I am new to lammps. I have a system with around 40000 atoms built by assembling two systems: NaCl electrolyte and crumpled graphene electrode. I have made electrolyte using avogadro and packmol, converted pdb to lammps data file using openbabel. I have made graphene sheet using Gopy…

Registered Dec 2023 1 day old *estimated Information on this page was last updated on Dec 12, 2023 About Lamz-Groups.club The domain Lamz-Groups.club belongs to the generic Top-level domain .club. It is associated with the IPv4 addresses 104.21.76.62 and 172.67.190.86, as well as the IPv6 addresses 2606:4700:3034::ac43:be56 and 2606:4700:3037::6815:4c3e. The…

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Hello lammps users,I am new to lammps. I have two questions. I have a system with around 40000 atoms. Will it take significantly less time if I run my simulation using mpi_run instead of serial_run? As I am running using the command “mpiexec -np 18 lmp -in NaCl.in” , I…

coldzer December 11, 2023, 2:12pm 1 Hello, I am trying to understand the line Loop time in the log file, how should I read it, so I can compare different runs? Loop time of 142.713 on 1536 procs for 103958 steps with 686818 atoms My understanding is that it took…

Hello guys,I’m trying to run a script for calculating phonons, after include phonon package within make yes-phonon and recompiling lammps via make serial.There is an unexpected error after run my script via …/lmp_serial -in in.phonon:Reading adp potential file …/…/…/potentials/Ni.adp with DATE: 2011-06-20ERROR: Unrecognized fix style ‘phonon’ is part of the…

Bo_Lin6 December 10, 2023, 1:04pm 1 Dear LAMMPS users, I’m a new beginner using LAMMPS for molecular dynamic simulation. I am currently working on modeling the sorption and diffusion between polyethylene and methane using LAMMPS. I obtained a polyethylene system from this source: Atomistic Deformation of Amorphous Polyethylene – EVOCDI…

Have you read the manual: Yes. I used the scripts from Lammps manualMD simulation experience: Yes, several years, with Gromacs, Amber and OpenMMLammps experience: No. Started recentlyLammps version: 20230208Lammps execution command: mpirun -np xxx lmp -in in.tip4pCan you provide your input scripts and results: Yes. Please check this: Input scripts…

sinail December 8, 2023, 11:39pm 1 We are having issues running coarse-grained simulation of a virion (~400,000 beads) in LAMMPS. We have been successfully running simulations with lmp_mpi, until the introduction of tabulated potentials in the bonds of specific flexible regions (~5,500 bonds). Now our simulations stop within minutes using…

Hello. I am trying to create a CH4 molecule file. I read through LAMMPS documentation and previous posts in the forum on molecule files. My current approach to this is to create a CH4 molecule file using a information in my CH4 data file manually. Currently, I have to put…

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Using Aug 2023 version of Lammps This is a rather basic issue. I am following the paper by Kim to model , water, ethahol and phosphoric acid adsorbed to TiO2 using their ff.Reactive MD-force field: Kim, S.-Y., van Duin, A. C. T., and Kubicki, J. D., 2012, Molecular dynamics simulations…

Hello, I am trying to run a peridynamics simulation where a cylinder rotated around the y-axis impacts a rigid plate. However, atoms on the rotated cylinder are being cut off at the bounding box of the original, unrotated region. I’ve been changing the size of the cylinder region to see…

Dear Lammps developers.I learned that free energy perturbation has been integrated within the scheme of lammps. Some machine learning potentials, such as deep potentials, eann, mace, etc. I wonder does fep can be applied to systems described by machine learning potentials.Best wishes,Peng diracliup: I wonder does fep can be applied…

Dear all I have a group called “type111” which has 10 atoms of type 1. I would like to print each of the ids of these 10 atoms, for which I use the command “compute 5 type111 property/atom id”, a loop of a variable “y” ranging from 1 to 10…

I am attempting to submit a Slurm script on my school’s clusters, aiming to perform LAMMPS calculations and post-processing with MPI-based parallel Python in a single script. However, I encountered an error. After experimenting, I have distilled the script to its minimal form that consistently triggers the error. my Slurm…

Noshin December 4, 2023, 4:47am 1 I have written a lammps script by lammps. I wrote to determine the chloride diffusion rate through nanopore of csh. I used Atomic style atomic and LJ force field. Now the issue is the diffusion rate of chloride ion and water ion is same….

dlee5 December 4, 2023, 2:37am 1 Hello, I am new to LAMMPS, and I am using the stable 2, August 2023 version. I am trying to build LAMMPS using make mpi, and I have the Molecule, Manybody, KSPACE, and Rigid packages installed. I am trying to install the Electrode Package….

Dear members of the LAMMPS mailing list, I have been attempting to build and install the LAMMPS Python interface (Pylammps) to leverage the advantages of accessing thermos data. However, I am encountering the following error: Based on my understanding from the documentation, if I set up a simulation with a…

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Hello everyone, I am currently using the stable version of LAMMPS as of August 2, 2023.In the previous version of LAMMPS, the ‘region’ keyword was not required when using the fix gcmc command to insert atoms throughout the box. However, I have encountered an issue when trying to use the…

Salad December 2, 2023, 6:43pm 1 I am simulating nanoimprint lithography of a gold substrate with a silicon mold. I’m new to lammps and cannot figure out how to link the two meam potential files of gold and silicon to their respective atom groups. If anyone would be kind enough…

This lesson provides an overview of some more advanced techniques and uses of LAMMPS. Specifically, we will be discussing: Measuring and improving LAMMPS performance: Strong vs weak scaling for a range of systems. Smarter domain decomposition. Accelerators, and what they do. Running LAMMPS from Python. Analysing systems through reruns. Advanced…

Greetings everyone, I have a query regarding the addition of an external force to the entire simulation box. Specifically, I’m interested in applying acceleration along any axis to the box. Is this achievable, and if so, how can it be implemented? Thank you. stamoor November 29, 2023, 12:42am 2 Not…

m.adibi November 28, 2023, 9:14pm 1 Greetings, I would like to calculate the Gibbs free energy using the Frenkel-Ladd path and the nonequilibrium implementation suggested by Freites et al. (2016) in this paper. I found that the free energy perturbation can be done using the fix ti/spring command in lammps….

Hello, community! I’m currently working on a molecular dynamics (MD) simulation using LAMMPS, and I’m looking for comprehensive guidance on visualizing and drawing the simulation results. Specifically, I’m interested in using VMD, Avogadro, or any other software that you would recommend. I’ve attached an example image of my simulation results…

Dear Deep, As the error says: USER-MISC does not exist! Depending on the LAMMPS version you have installed, they might have changed the name of the package. Please take a look at the LAMMPS documentation. “Also attached lammps dat_min for 21 degree (MoS2/without_python/near_0) from this compiled version of Lammps….

molecular dynamics – Free energy calculations for lammps – Matter Modeling Stack Exchange Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Visit Stack Exchange Log in Sign…

Monoj November 27, 2023, 12:11pm 1 Dear LAMMPS Community, I am currently trying to perform a hybrid MD-MC simulation for a polydisperse LJ liquid. To achieve this, I am using the “sphere” atom type, allowing me to input the radius of the particles. The corresponding pair is computed using the…

I hope you’re doing well. I’m currently working on a project that involves running a LAMMPS input script from within a C++ program on Windows. I’ve been trying to figure it out on my own and have read through various resources, but I seem to have hit a dead end….

phd – How to do free energy calculations in lammps? – Academia Stack Exchange Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Visit Stack Exchange Log in…

i have the next lammps archive ####geometriavariable rout equal “40/3.560” ### cambiar el primer numero, por### el valor de Re pedidovariable lboxp equal “v_rout+7”variable zwall equal “v_pinit”variable poswall equal “-v_rout-1”#-v_sigma(18/60)^(1.0/6.0)”*variable poswallup equal “v_rout+1”#-v_sigma(18/60)^(1.0/6.0)”* clearunits metaldimension 3boundary p p patom_style atomic lattice fcc 3.560 #origin 0. 0. 0.#region 1 block -32…

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state…

hgc November 23, 2023, 2:18pm 1 Hi all, The explanation of the fix move command in the manual is as follows: The units keyword determines the meaning of the distance units used to define the linear velocity and wiggle amplitude and rotate origin. This setting is ignored for the variable…

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/beefy16/data/132amd64-default/5b346a1c0cc2/logs/votca-2023.log Build URL: pkg-status.freebsd.org/beefy16/build.html?mastername=132amd64-default&build=5b346a1c0cc2 Log: =>> Building science/votca build started at Tue Nov 21…

Dear All, I am using LAMMPS (23 Jun 2022) I need to use Extra-fix package.I have used “make ps” command to figure out if the package exists or not, but I got the error make: ” *** No rule to make target `ps’. Stop. ” , which means I am…

I am trying to simulate radiation damage behavior where I am depositing both electron and lattice temperature in the structure. I’m simulating in the super computer. But I always have the out of memory error. I tried simulating 100x100x1, 50x50x1, 10x10x1 electron grids, they all give the same errors. The…

Hi everyone! I want to model a Coulomb system using the pure Ewald potential, without any modifications such pppm/wolf etc. Could you please tell me where to find the maths that is implemented in pair_coul_long.cpp, especially information about the tabular data for the long-range part? KT_Boltsman: Could you please tell…

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cara November 19, 2023, 2:13pm 1 Hello all,I want to get the parameters of OPLS-AA force field for a organic molecule(sulfobetaine) and then simulate in LAMMPS. I know there is a oplsaa.lt file under the installation directory of Moltemplate, but there are so many types to look up and it…

I’ve created a structure of water droplet falling into Cu surface using material studio. I’m trying to convert material studio file using msi2lmp into lammps lmp data file. But, I’m getting this: Running msi2lmp v3.9.9 / 05 Nov 2018 Forcefield: Class IForcefield file name: /usr/share/lammps/frc_files/cvff.frcOutput is recentered around geometrical centerOutput…

This fix performs grand canonical Monte Carlo (GCMC) exchanges of atoms or molecules with an imaginary ideal gas reservoir at the specified T and chemical …Introduction¶. Grand Canonical Monte Carlo (GCMC) is so named because it allows sampling from the grand canonical ensemble. In NVT we couple the simulation …4 apr. 2018…

Intel kicked off the Supercomputing 2023 conference with a series of high performance computing (HPC) announcements, including a new Xeon line and Gaudi AI processor. Intel will ship its fifth-generation Xeon Scalable Processor, codenamed Emerald Rapids, to OEM partners on December 14. Emerald Rapids features a maximum core count of…

Extending and Modifying LAMMPS Writing Your Own Source Code: A pragmatic guide to extending LAMMPS as per custom simulation requirements by Dr. Shafat Mubin, Jichen Li, Dr. Steven PlimptonEnglish | February 19, 2021 | ISBN: 1800562268 | 394 pages | PDF | 55 Mb Understand the LAMMPS source code and…

AMINA November 15, 2023, 10:20am 1 hello,I am simulating cacao butter which contain 3 triglyceride with different proportion (POS 48%, SOS 34%, POP 18%)Can you please tell me if there is any command which can do thisRegards,amina This is not a question that can be handled with a LAMMPS command….

Hi!I want to compute dipole moment as sigma(qi*ri) by using variable of atom style however I am getting an error of “Substitution for illegal variable Mnew”. Here are my lines from the code:variable charge atom “q”variable x1 atom “xu”variable y1 atom “yu”variable z1 atom “zu”variable r1 atom “v_x1+v_y1+v_z1”variable Mnew atom…

Hi Team I am trying to validate the floating point difference for comparing the benchmarks with various compiler. Currently I have two question. For intel package ,GCC is not working properly. What is the accepted choice of compiler for benchmarking in.rhodo.scaled and in.lj dataset for intel Package? For in.rhodo.scaled and…

Hello everyone.I want to create graphene layers and then cut an atomic system, using a 3-D shape defined in an STL file by using Atomsk (follow this tutorial Atomsk – Tutorial – Using 3-D Models in STL format). Then I import this atomic system into LAMMPS but the file only…

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Xtof November 14, 2023, 8:00am 1 Dear all, Would anyone know where to find the potential for Y-H? I found some potential for Y-Y in an article from 2013 but so far nothing about Y-H. Many thanks in advance and best regards,Christophe It’s good practice to reference the articles you…

Intel has unveiled additional details about its upcoming 5th Gen Xeon processors. Codenamed Emerald Rapids, these CPUs are architecturally identical to Sapphire Rapids but pack more cores and cache on the same platform. More specifically, the new Xeon Scalable chips will offer up to 448MB of L3 cache, thrice as…

Intel has unveiled the latest performance and internal projections of its upcoming 5th Gen Emerald Rapids & next-gen Granite Rapids Xeon CPUs. Intel 5th Gen Emerald Rapids Xeon 64-Core CPU Offers Up To 40% Better Performance Than 56-Core Sapphire Rapids Talking about its Xeon CPUs during SC23, Intel unveiled new…

Dear Dr. Artrith and team, Greetings! I’m new to aenet. Thank you Dr. Artrith and team for develping aenet and opensourcing it.  I downloaded USER-AENET and interfaced with lammps 4Feb2020-version. However, I’m getting the following error (complete error response attached ) when I compile the lammps using “make mpi”. Kindly…

I’m seeking clarification on the selection of suitable boundary conditions for simulating shear deformation of a screw dislocation using LAMMPS. In my script, I currently employ the following commands: lammps fix 1 upper setforce 0.0 0.0 0.0 fix 2 lower setforce 0.0 0.0 0.0 fix 3 upper move NULL ${strainrate}…

I want to read a lammps data file in ASE, for instance the TIP3P or the SPC model. The lammps examples provide the input script and the data file, which work perfectly. ASE is not able to read the .mol file: it cannot parse neither Shake *** nor Shake ***…

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere3/data/132arm64-default/d5268d5f7157/logs/votca-2022.1_1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=132arm64-default&build=d5268d5f7157 Log: =>> Building science/votca build started at Fri Nov 10…

I want to simulate some water in MD with ASE and a LammpsLib calculator. I set up a minimal Lammps calculator and I try to calculate the energy per atom of an isolated molecule, and a 3x3x3 supercell. I get different energies. Question 1: How is it possible? Moreover, when…

Hello,I want to read a LAMMPS xyz file into a pipeline using python and then remove some frames and save it again?Any idea is appreciated.And how can create a LAMMPS restart file from a specific frame?Thank you Hi, Please have a look at this section in the OVITO python reference:…

I am following the deepmd-kit documentation to implement this kit into a plugin version of LAMMPS, the documentation I am using is found here and here. I am close to completing everything, but am having issues when trying to install the deepmd-kit C++ interface. I know from the documentation, I…

Hi everyone, I am trying to run a fix reax/c/species command but I want the atoms in the group to be reassigned periodically. Unfortunately, reax/c/species doesn’t allow the use of a dynamic group of atoms. Is there any other command I could use or any other way I could approach…

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Greetings, I setup a simulation to calculate CO2 properties using the known EPM2-flexible model. My system has 1000 CO2 molecules.The forcefield parameters are as below:In system.in.init: units real atom_style full bond_style harmonic angle_style harmonic pair_style lj/cut/coul/long 10.0 kspace_style pppm 1.0e-5 pair_modify mix arithmetic In system.in.settings: bond_coeff 1 1283.381 1.149 angle_coeff…

Dear lammps users, I would like to count the number of atoms when velocity of particles meets the certain conditions. I used below command to accheive it. compute avejVztip3p tip3p reduce/region interest ave v_jVzAtomfix trap_v all ave/time 10 1000 10000 c_avejVztip3pvariable trap_velocity equal f_trap_vif “${trap_velocity}< 35” then “variable num_na equal…

Hi Lammps Community Im trying to do energy minimization of a ternary alloy and the potential i have been using is hdnnp(high dimensional neural network potential). This is just a small task to check the proper working and get familiar with hdnnp. Later on I will be conducting MD simulations…

How to simulate polyethylene using Reacter? Version: LAMMPS (3 Nov 2022) the input file are attached on dropbox Dropbox c2h4.tar Shared with Dropbox Liang_Xu: the input file are attached There are no attached files. To avoid spam abuse of the forum, new accounts are not permitted to attach files. So…

Nope, still can’t post.pastebin.com/uXpAuPnySidenote, Pastebin flagged it as potentially harmful…Edit: I could only post it as private, I’m linking here instead. LAMMPS (2 Aug 2023 – Development – patch_2Aug2023-427-g75682ffbca) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task package gpu 0 echo…

molecular dynamics – How to extract Lindemann Index from LAMMPS dump files? – Matter Modeling Stack Exchange Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Visit Stack…

Hi,I am using LAMMPS to perform coarse-grained particle dynamics simulations of biological cells and tissues. I am using LAMMPS version – 29 October 2020. I am using compute stress/atom to find out the spatial distribution of stress inside the subcellular space. There is only pairwise interaction in my simulations because…

Hello, I coded up my own version of Stillinger-Weber silicon using the default parameters in LAMMPS. At equilibrium my code produces the exact same value as LAMMPS; however, once I include dynamics there is a noticeable gap between my implementation and LAMMPS. I am not asking for anyone to debug…