Tag: LAMMPS

Create model – LAMMPS General Discussion

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…

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Variable Stiffness Particles using GRANULAR package – LAMMPS Beginners

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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Molecular Dynamics Software Market to Witness Revolutionary

Molecular Dynamics Software Market Global “Molecular Dynamics Software Market” Research report is an in-depth study of the market Analysis. Along with the most recent patterns and figures that uncovers a wide examination of the market offer. This report provides exhaustive coverage on geographical segmentation, latest demand scope, growth rate analysis…

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Error in neigh_modify configuration – LAMMPS Beginners

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…

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A question for the ‘fix evaporate’ command – LAMMPS Beginners

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…

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Can’t Access Multiple GPUs when Using PPPM GPU Acceleration – LAMMPS

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,…

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Division of the box into smaller regions – LAMMPS General Discussion

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…

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Adding an atom onto a surface while using fix wall/region – LAMMPS Beginners

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…

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Single atom in a box (lammps)

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 #…

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Generating water-heavy metals box using atomsk – LAMMPS Beginners

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…

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LAMMPS Element Mapping – LAMMPS General Discussion

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…

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Harmonic bond lammps – LAMMPS Beginners

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…

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Group/group and pe/atom pair is evdwl + ecoul + elong? – LAMMPS

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…

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Moltemplate: Number of dihedrals in data file output – LAMMPS General Discussion

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…

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How to eliminate adsorption on rough walls – LAMMPS General Discussion

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…

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Sorting atoms based on their Atom ids – LAMMPS Development

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…

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Particle concentration increase near harmonic wall – LAMMPS

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…

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About the pair style of ideal gas – LAMMPS General Discussion

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,…

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Dihedral atom missing error on lammps – LAMMPS

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…

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Two uloop variables? – LAMMPS

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…

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Angle_coeff of H2O in examples/template 109.47 not 104.45 degrees? – LAMMPS Beginners

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…

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Only apply forces in x and y direction but a z direction motion shows up – LAMMPS General Discussion

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…

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Multipli fix ti/spring commands – LAMMPS

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…

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Silicon Oxide Structure – LAMMPS

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…

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Optimizing pair style with GPU – LAMMPS Development

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…

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Topic Templates – LAMMPS General Discussion

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…

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Potential energy associated with a molecule – LAMMPS

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…

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ERROR: Unrecognized fix style ‘press/langevin’ – LAMMPS

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…

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Checking my installation via serial mode of testing – LAMMPS Installation

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:…

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How to write total potential energy to dump file? – LAMMPS Beginners

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…

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Energy Minimization while Simulating Supercapacitor Electrode using Constant Charge Method – LAMMPS General Discussion

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…

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Lamz-Groups.club – Main

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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A Comprehensive Overview for the 2024-2031 Period| With 117 Pages

PRESS RELEASE Published December 12, 2023 Latest Research Report On “Molecular Dynamics Simulation Software Market” 2024 Analysis, Future Projection, Forecast By 2031 | With {117} Pages Global “Molecular Dynamics Simulation Software Market” Research Report 2024-2031 is a factual overview and in-depth study of the current and future market of the Molecular…

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Mpi_run aborts with abort code 1 – LAMMPS General Discussion

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…

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How to understand Loop time? – LAMMPS

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…

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Fix Phonon error after running script – LAMMPS General Discussion

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…

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What the most accurate potential to use for the simulation of gas diffusion in PE? – LAMMPS General Discussion

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…

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Huge Etotal difference between TIP4p implicit VS explicit methods from the manual script – LAMMPS Beginners

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…

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Issues with bond_style_table – LAMMPS

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…

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CH4 Molecule file – LAMMPS

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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Molecular Dynamics Simulation Software Market Worth Observing Strong Growth by Abalone, Software for Chemistry and Materials (SCM), Ascalaph Designer

The Molecular Dynamics Simulation Software Market research report provides all the information related to the industry. It gives the market’s outlook by giving authentic data to its client which helps to make essential decisions.  It gives an overview of the market which includes its definition, applications and developments, and manufacturing…

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Molecular Dynamics Software Market Comprehensive Analysis by Abalone, Software for Chemistry and Materials (SCM), Ascalaph Designer

A2Z Market Research recently published its latest research study on the Global Molecular Dynamics Software Market, comprising over 130+ pages of analysis on the business strategies adopted by both key and emerging industry players. The report provides insights into the current market development, landscape, technologies, drivers, opportunities, market outlook, and…

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How to group atoms as molecules in reax – LAMMPS General Discussion

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…

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LAMMPS region rotate cuts off created atoms – LAMMPS Beginners

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…

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Does free enery perturbation can be applied to the system described by deep learning potential model? – LAMMPS Development

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…

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Obtain ID atoms belong to a Group – LAMMPS General Discussion

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…

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linux – MPI_Init_thread Error When Integrating LAMMPS and Parallel Python in Slurm Script

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…

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Trouble finding water diffusion – LAMMPS Beginners

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….

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Trouble installing Electrode Package using traditional make – LAMMPS Installation

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….

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Issue with Accessing Thermo Data in Pylammps – LAMMPS Installation

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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Molecular Dynamics Software Market Analysis, Future Demand, and Global Industry Forecast to 2030 |Abalone, Software for Chemistry & Materials (SCM), Ascalaph Designer, Avizo (Software), CHARMM

A2Z Market Research has published a report that represents the process of collecting, analyzing, and interpreting data about a Molecular Dynamics Software market. This is a crucial step in developing a business strategy or launching a new product, as it helps companies to gain a deeper understanding of the Molecular…

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ERROR fix gcmc region extends outside simulation box – LAMMPS General Discussion

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…

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Linking multiple potential files to two different atom regions – LAMMPS Beginners

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…

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Advanced use of LAMMPS

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…

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I need to give a force to the simulation box – LAMMPS Beginners

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…

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Can use fix/ti spring for any type of crystalline structure? – LAMMPS

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….

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Seeking In-Depth Advice: Drawing Lammps MD Simulation with VMD, Avogadro, or Alternatives – 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…

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Modified LAMMPS installation errors

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….

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molecular dynamics – Free energy calculations for 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…

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Problem regarding fix atom/swap – LAMMPS Development

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…

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Help Running LAMMPS Input Script in C++ on Windows – LAMMPS Development

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….

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phd – How to do free energy calculations in lammps?

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…

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Ovito only reads 1 frame of a lammps dummp – OVITO

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…

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LAMMPS – HPC Cineca

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…

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Fix move variable – LAMMPS

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…

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132amd64-default][science/votca] Failed for votca-2023 in package

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…

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How to check if the EXTRA-FIX package exists in my installed lammps and how to install it – LAMMPS Beginners

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…

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Issue with fix ttm/grid – LAMMPS

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…

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coul/long – LAMMPS Beginners – Materials Science Community Discourse

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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What is LAMMPS? | 3 Answers from Research papers

How does the amount of time spent kneading dough affect the final product? 3 answers How to design mobile application for motorcycle users? 5 answers What are the different innovative binder modification strategies for improved RAP pavement performance? 3 answers Does the addition of retarders reduce the plastic viscosity of…

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OPLS-AA force field – LAMMPS General Discussion

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…

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Materials studio to lammps data file – Materials Project

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…

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Gcmc Lammps Tutorial – Trkoreansjj

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…

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Intel updates HPC processor roadmap

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…

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Extending and Modifying LAMMPS Writing Your Own Source Code / AvaxHome

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…

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Multiple systems in a single simulation – LAMMPS Beginners

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….

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Computation of dipole moment through variable command – LAMMPS General Discussion

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…

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Lammps result validation – LAMMPS Development

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…

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Graphene from Atomsk to LAMMPS, Material Studio – LAMMPS Beginners

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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What are the newest articles about self-propelled particles in confined channels studied by LAMMPS?

How can the expansion planning of active power distribution networks be made more efficient? 5 answers How can Eulerian Video Magnification be applied to water resource management? 3 answers What are the newest articles about self-propelled particles in confined channels? 5 answers What are the most effective unlearning mechanisms for…

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Potential Y-H? – LAMMPS General Discussion

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…

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Intel Xeon Emerald Rapids-SP to Offer 40% More Performance than Sapphire Rapids in AI

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…

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Intel 5th Gen Emerald Rapids 64-Core & Granite Rapids Xeon CPUs Performance Unveiled

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…

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Error in compiling lammps after interfacing with AENET

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…

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molecular dynamics – What are the appropriate boundary conditions for simulating shear deformation of a screw dislocation in LAMMPS?

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}…

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molecular dynamics – Read and run lammps water model in ASE

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 ***…

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132arm64-default][science/votca] Failed for votca-2022.1_1 in build

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…

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Water simulation in ASE/LAMMPS – Matter Modeling Stack Exchange

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…

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Modifying pipeline – OVITO – Materials Science Community Discourse

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:…

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molecular dynamics – Issue building deepmd kit for a plugin version of LAMMPS

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…

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Using reax/c/species with a dynamic group – LAMMPS General Discussion

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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Molecular Dynamics Software Market Is Booming Worldwide

Report Description: Global Market Vision has rolled out a new report namely Molecular Dynamics Software Market that integrates crucial insights on the market. The report supplies a comprehensive analysis of business aspects like market size, competitive scenario, market opportunities, market shares, and revenue growth patterns, and the volume and value…

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EPM2 model does not reproduce literature data – LAMMPS General Discussion

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…

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Using if command in Lammps – LAMMPS

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…

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Lammps Error: Illegal pair_style hdnnp – LAMMPS General Discussion

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…

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Simulating polyethylene using REACTER – LAMMPS General Discussion

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…

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Optimizing LAMMPS for my purposes – LAMMPS Beginners

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…

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molecular dynamics – How to extract Lindemann Index from LAMMPS dump files?

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…

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Sign of per atom stress computed by LAMMPS – LAMMPS General Discussion

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…

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Pair style sw vs. My Implementation – LAMMPS General Discussion

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…

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