Lammps pressure nan. I try to use finite difference to approximate derivative.

Lammps pressure nan While running for NVE simulation on the following system: lignin + 500 ozone + 3500 water for 1 ns and 0K starting temperature, Hi, I noticed that for an example of the bulk liquid water MD simulation at ambient conditions there is a discrepancy between the pressure that is evaluated directly from LAMMPS Press variable and the from diagonal components of the stress tensor. I have tried various damping parameters varying from 1-10000 on press/berendsen and 1-100 on temp/rescale (using fix nve for integration). Expected Behavior. Dear Lammps users, I have a quick question about how lammps calculate the pressure. explained, I get energy and pressure as 'nan'. similarly, for coulomb, the pressure becoming NaN, i. dynamics. 1000100 3. 00000000000000e+00 -nan 1000400 3. However, I got a negative value no matter the difference formulas used including forward, backward and central difference. If Then, relax the gas system in this sealed container under -30 degree centigrade. If a mapping value is specified as NULL, the mapping is not performed. 75193022228514e+00 3. zero or more keyword/value pairs may be appended. in' with the last version of lammps (5nov2016). The rotational kinetic energy is computed as \(\frac12 I \omega^2\), where \(I\) is the moment of inertia tensor for the aspherical particle and \(\omega\) is its angular velocity, which is computed from its angular momentum. I saw that two thoils are moving away Hello all, I’m using LAMMPS (2 Aug 2023 - Update 3) on my Macbook M2. I’m working on creating a crystalline ice at 1 K (H2O) in lammps using the TIP3P potential. A compute pressure may be used for that purpose. It is used primarily for calculating the gradient of energy, force, and stress components with respect to model parameters, which is useful when training mliap pair_style models to match target data. All steps are simple. 00000000000000e+00 -nan 1000200 4. 7922 10 -nan -nan 10 0 15 this is incorrect syntax for fix npt. For all units except lj, LAMMPS uses physical constants from www. In other windows without Description . By default, this compute is created with a simple compute temp (see the last argument of the compute pressure command), which is used to calculated the kinetic component of the pressure. Helfrich. 2. as mentioned in the previous e-mail, you still have coulomb interactions. Even if the minimization ID, group-ID are documented in fix command. reax lmp_control two cases (say LJ and EAM-morse-LJ) but for ReaxFF after few ps it gives me nan, even I reduced the time step but still i am getting nan. If you see wild thermodynamic values or NaN The normalize/pressure keyword changes how box dimensions evolve when using the pressure or pressure/mean deformation styles. After energy minimization, I was trying to equilibrate my system with NPT ensemble at 300 K at P=0 with “metal” units. Ideally, the two results should be identical. So, I am using this command fix 1 all press/berendsen iso 1 1 1000 fix 2 all nvt temp 300 300 100 but in output, I Dear Users, I find a bug in the pressure evaluation when running the attached script 'lammps. Ti_lattice), I get NAN values for the energy and the pressure: Step Temp E_pair E_mol TotEng Press Volume 0 0 nan 0 nan nan 73353. When I try to simulate the slab in water. Restart files also store this setting. Define a computation that simply stores rigid body attributes for rigid bodies defined by the fix rigid/small command or one of its NVE, NVT, NPT, NPH variants. NaNs is just the consequence. A negative pressure simply means that on average lammps运算报错Non-numeric pressure - simulation unstable 怎么解决啊in文件图,计算化学公社 . Compute style mliap provides a general interface to the gradient of machine-learning interatomic potentials with respect to model parameters. (Note for Non-LAMMPS users, the damp parameters give the amount of time for that property to relax). cpp:1089) Because of that error, I have to restart my simulations from a restart file to continue my simulations. 3794046816. I also need to know how the pressure changes on each side of the membrane with respect to the time. This allocates a storage buffer and copies the C-style or C++ style string into it. Can you This command is used to compute the pressure tensor in the reference frame of the applied flow field when fix nvt/uef or fix npt/uef is used. Check the New features and bug fixes section of the LAMMPS WWW site to see if the bug has already been reported or fixed or the Unfixed bug to see if a fix is pending. keyword = pos or vel or ramp or temp or units pos args = z z = z coordinate at which the piston begins (distance units) vel args = vz vz = final velocity of the piston (velocity units) ramp = use a linear velocity ramp from 0 to vz temp Navin, There's a big difference between calculating the stress and prescribing it. 0. I am running a test setup in LAMMPS. The barostatting fixes can also use temperature computes that Dear All I am simulating gold nanoparticle with hexanthiol using ReaxFF. See the compute temp/body and compute pressure commands for details. After I ran NVT or NPT simulation at 273K and 1 bar for relaxation, I tried to swap Zr atoms with Y atoms in the same ensemble. while the pressure increases (becomes more positive) and visually (via VMD) the mineral collapses and LAMMPS reports the result at step 1 is “nan” for the SHAKE stats and for the themo output. Set the dimensionality of the simulation. LAMMPS is not going to do very well at minimizing with bad forces. I am sure that their is no atom overlap in the initial configuration. I used the primitive cell of CaO to expand the cell and then created a cylindrical channel in the middle, filling it with CO2 using Packmol. 0 0. fix 1 all npt temp 10 10 0. 在1月14-20日期间，本论坛仅限等级≥level 4的成员发贴，带来的不便请谅解！其他成员若有学术问题请等到能发贴的时候再发帖。 Just as picture above, the temp is generated every 10000 timesteps, however, the compute command runs every timestep. I have tried different ways and also tried to find answer in the mail list, but I failed. Dear all, I would like to know how to apply a pressure difference to a group of atoms? Suppose I have a water slab which is periodic in x and y dimension, now I’d like to apply, say, 2 atm pressure to the slab along z axis in the positive direction, while apply, 1 atm pressure to the slab along z axis in the negative direction. that the computed pressure can be Nan because of a division by zero. ch), Xuejin Li et al at the USI, Switzerland and Brown Description . If the sub-style is used more than once, an additional number nsub has to be specified in order to choose which instance of the sub-style will be used by the compute. Alternatively, you can directly assign a new compute (that calculates pressure) which you have defined, to be used for calculating any thermodynamic quantity that requires a lammps运算报错Non-numeric pressure - simulation unstable 怎么解决啊in文件图,计算化学公社 . (the neighbor list doesn’t use gpu-accelerate, also I check the gpu The second Hf argument maps LAMMPS atom type 2 to the Hf element, and the third O argument maps LAMMPS atom type 3 to the O element in the potential file. After I finished the step of minimization and eveythings looks okay here, I would like to make the thermal equilibrium of the system that I use the command as “fix 1 all npt temp Hello all, I am running molecular dynamics simulations in lammps and trying to calculate how polydispersity affects the pressure. A common choice is to use \(M_i = m/P\), which results in the mass of the entire ring-polymer being equal to the real quantum particle. if it has a positive pressure it “wants to expand”. gov. The system need to be at equilibrium at $\pu{10K}$ and for this I am giving initial velocity at $\pu{10K}$ and running NVE for short duration of $\pu{2ps}$ ($\pu{1fs}$ timestep) followed by NPT at $\pu{10K}$ for $\pu{20ps}$. Hi Axel. By default LAMMPS runs 3d simulations. Style cg is the Polak-Ribiere version of the conjugate gradient (CG) algorithm. lykov at usi. The NULL values are placeholders for Description . None of the fix_modify options are relevant to this fix. The machine on which things work yields $ uname -a Linux mc1 3. I try to use finite difference to approximate derivative. 89 August 2015 LAMMPS Users' Workshop and Symposium . currently, I am trying to modeling polymer system for preliminary study of LAMMPS. If I want to simulate a system that contain mW water with Sw potential and also hybrid with lj potential with other type particle everything is ok when I just use mpi run this system but when i try to use gpu to accelerate, the thermal output like LAMMPS Mailing List Mirror. pressure_to_lammps() contains the following Note. However, when I run my simulation with a ReaxFF which is not included in LAMMPS (C/O/H/F/Li/S force field) I get “NaN” for pressure. 0 ~ 20. While running for NVE simulation on the following system: lignin + 500 ozone + 3500 water for 1 ns and 0K starting temperature, Alternate means of relaxing a system are to run dynamics with a small or limited timestep. Illegal arithmetic can cause LAMMPS to run slow or crash. When using this keyword, the compute must be first active (it must be included via a thermo_style custom command) while the atoms are still at their lattice sites (before equilibration). The most commonly used units are metal, since the internal units of distance, energy, force, and charge in DeePMD-kit are \AA, eV, eV / \AA, and proton charge, respectively. I made data file which the coordinate information was obtained from the published paper. 00000000000000e+00 -nan. On one machine I get reasonable answers, while on the other I get nan. the most common causes for NaN are bad geometry, bad/unsuitable force field parameters, and too large a time step. e. The keywords and output information are documented in compute_pressure. currently, I am trying to modeling polymer system for preliminary study See the compute pressure command for details. The analog for an energy minimization is the fix box/relax command. I have downloaded and build a large cell of over 1500 water molecules with bond and angles included in the file description. when your system has a negative pressure it “wants to shrink”. The second is that the dummy site has to be reset after the neighbor lists are build in the compute_outer pressure becoming NaN, i. 97 302. Dear All, I am using Lammps (lammps/29sep2021) to compute the stresses and the pressure: I did the following: variable pr equal press/10000 variable sxx equal pxx/(10000) variable syy equal pyy/(10000) variable szz equal pzz/(10000) variable sxy equal pxy/(10000) variable sxz equal pxz/(10000) variable syz equal pyz/(10000) velocity all create 300. By playing a bit with the parameter file, Summary. LAMMPS Version and Platform. Thank you. However, I approached a problem that the fluctuating pressure in each step of optimisation and importantly the final step of the optimisation does not have the value of pressure that I set. I can suppress this fluctuation by introducing drag term to Nose-Hoover equation: Input. LAMMPS Mailing List Mirror. test (1. Hi Lammps users, I’m trying to simulate the reaction between CaO and CO2 using reaxff. Bingyu_Cui November 12, 2017, 12:12am 1. Topic Replies Views Activity [lammps-users] executing lammps from a mac. The followings are the codes and errors. It most probably means you have bad dynamics. 3 KB) data. This is basically a thermodynamic question, but goes into how LAMMPS calculates the necessary I have a Flare++ generated LAMMPS potential with the following header: DATE: Thu Sep 15 08:15:18 2022 CONTRIBUTOR: Martin Siron 2 chebyshev 2 15 3 1730730 quadratic 7. 00000000000000e+00 -nan 1000500 3. To run a 2d simulation, this command should be used prior to setting up a simulation box via the create_box or read_data commands. reax. I don’t quite get what you are trying to do with this script. These per-atom values could be summed for a group of atoms via the compute reduce command. These units are consistent with the metal units in LAMMPS. From NIST database, knowing the density of the system from the simulation, I know that I should get from LAMMPS a pressure of 3 atm. -K. Does anyone know how to reduce fluctuations? Please PDF | On May 8, 2019, Sumith Yesudasan published Thin Film Pressure Estimation of Argon and Water using LAMMPS | Find, read and cite all the research you need on ResearchGate At NPT, the pressure is very good, near 100 atm without big fluctuations. I number of atoms is not large enough, the pressure can not be calculate correctly. If not, send an email to the mailing list describing the Dear lammps users, I would like to simulate point defects in YSZ, Y stabilized ZrO2. If one wants to use other units like real Dear Lammps-users, Recently I start using lammps to to molecular dynamic study on cement (C-S-H). style_name = nvt or npt or nph one or more keyword/value pairs may be appended. . Even if the minimization A symmetric tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure tensor by the compute pressue command. Steve Hello lammps-users, I am simulating methane and water in a cube of 20 Angstrom to study their interactions. however, the pressure you apply with fix npt is an “external” pressure. I have modeled my code after the one at 8. ERROR: Unrecognized pair style 'reaxff' is part of the R The dtype=float will convert all Nones to nans and in pyiron. But the simulation gives my ‘NaN’ values for the thermo_style output values. As discussed on the Commands parse doc page, an input script can use “immediate” variables, specified as $(formula) with parenthesis, where the numeric formula has the same syntax as equal-style variables described on this page. A symmetric tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure lammps-users: I constructed a simulation system which contains 277696 atoms, the output after calculation is nan except volume and the first few lines of temperature. when I did the NPT equilibration (using Barendsen and 1 bar pressure), there is NAN r Dear all, I’m a (very) beginner in using LAMMPS. This allows the box size and shape to vary during the iterations of the minimizer so that the final configuration will be both an energy minimum for the potential energy of the atoms, and the system pressure tensor will be close to the specified external tensor. Yet they constantly differ by a factor ~ 340 atm(the one predicted by compute stress/atom is higher). I am trying to simulate calcium carbonate crystal slab in water using reax/c. 4. 81480499193611e+00 3. The simulation is very simple, and I want to see the increase of water temperature. As mentioned in the document this fix does NOT perform time integration. I convert eV to My model simulation is composed of a polymer-ion system including C/H/O/N/Li/S/F. I used the following commands but the pressure during simulation is extremely high and was equilibrated P=3800 bar. The buffer is allocated with “new” and thus needs to be deallocated with “delete[]”. The same might be true for calc_minimize(), but I didn't encounter this, yet. I am using $4000$ atom hcp system with MEAM potential. 3. 89272402639424e+00 3. These values can be used by any command I'm trying to do NPT calculations in LAMMPS using pair_allegro, but the Allegro model I trained is predicting -nan for the system pressure, so the NPT run fails. The density that I use for packing is calculated from an EOS derived from MC simulations of liquid water. Examples This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. However, I have encountered some errors when setting the velocity of the top several layers of particles using the “fix move” or “velocity set” command. Dear Lammps users, I’m trying to generate the potential files for the 2nn meam for the FeTiC system as described in Kim, H. nvt/sllod = style name of this fix command. Actual Behavior. Hi list, I used MAPS to build structure of a glycerol, then mininized the structure. 90598924756570e+00 3. non-numeric. potentials defined you need to investigate systematically what is wrong by turning off any unneeded tasks. The kinetic contribution to the pressure tensor will be accurate only when the compute specified by temp-ID is a compute temp/uef. I get ‘NaN’s in my log file for temperature and total energy and pressure. the minimum that should be possibly is a “run 0” command with “fix nve” and no other fixes. I wonder if you could give me some Hi, I noticed that for an example of the bulk liquid water MD simulation at ambient conditions there is a discrepancy between the pressure that is evaluated directly from LAMMPS Press variable and the from diagonal components of the stress tensor. This fix does not initialize a net flux through a system, it only conserves the center-of-mass momentum that is present Public development project of the LAMMPS MD software package - lammps/src/compute_pressure. Now I tried to run with the input script, but I got 'nan' in E_mol, Totla energy and pressure If you don't mind, This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1–6. You define: an npt fix, which is an integrator; a shake fix that is a modifier; as well as a timestep and reset the timestep value. face = zlo zero or more keyword/value pairs may be appended. I want a configuration where system is at It is only enabled if LAMMPS was built with that package. keyword = pair or shift or mix or table or table/disp or tabinner or tabinner/disp or tail or compute or nofdotr or special or compute/tally or neigh/trim pair value = sub-style N sub-style = sub-style of pair hybrid N = which instance of sub-style (1 to M), only specify if sub-style is used multiple times mix value = geometric or arithmetic or The anharmonic keyword will instruct the compute to return anharmonic properties rather than the full properties, which include lattice, harmonic and anharmonic contributions. goldnp_hexan_nonbond ffield. Are the atoms placed too close? ( I have tried with different box sizes varying from 10 angstrom to 30 angstrom) you can easily measure compute the distance and judge yourself. LAMMPS Mailing List Mirror _1185201182 October 25, 2016, 8:24am 1. if that pressure is The simulation will start, but immediately the pressure becomes nan. All units in LAMMPS except lj are supported. My input script is attached below. I am using “real” unit in my simulation. I also tried to fix pressure at 1atom before fixing temperature, but then it look at your pressure! for two molecules in a large box, it is *huge*. To start, I ran MD simulations with the repulsive part of the Morse potential with a small damping factor, with the goal of replicating Brownian Dynamics. For any given potential, such as SPC/E, both pressures are expected to be exactly the same at any given time. 回复： The temperature, press and total energy output are"-nan", what is wrong? LAMMPS. hns (C/H/O/N force field) from LAMMPS example. I am very confident with my preparation stage, and I follow a very strict scheme to properly equilibrate and relax my samples. A Nose-Hoover barostat will not work well for arbitrary values of Pdamp. The choice you make for units simply sets some internal conversion factors within LAMMPS. Related commands compute pressure, fix nvt/uef, compute temp/uef. I need to understand how to calculate the pressure in both sides of the membrane and consequently the drop across the membrane. Note that you can minimize some atoms in the system while holding the But you said the pressure in the system is negative or NAN. cpp at develop · lammps/lammps LAMMPS can be run on multiple partitions via the “-partition” command-line switch as described in this section of the manual. You can change the attributes of this pressure via the compute_modify command. The flux can be conserved in any combination of the directions, x, y, or z, using xflag,yflag,zflag. After the full relaxation, how to calculate the pressure of gas in the container under -30 degree centigrade? Is it possible to do the pressure statistic with molecular dynamic simulation; such as LAMMPS? Would anyone please give me some suggestions? Thank you in 11 Nov 2012. I do not know how to calculate dH/dT in a proper way. The formula for the components of the tensor is the same as the above expression for \(E_\mathrm{kin}\) , except that the 1/2 factor is NOT included and the \(v_i^2\) is replaced Navin, There's a big difference between calculating the stress and prescribing it. It is not necessary to use this command to compute the scalar value of the pressure. Check the mailing list to see if it has been discussed before. 0 1972 Pressure in LAMMPS (and in MD in general, as far as I know) is calculated based on the virial, roughly speaking the forces between the particles. If Pdamp is too small, the pressure and volume can fluctuate wildly; if it is too large, the pressure will take a very long time to equilibrate. While running for NVE simulation on the following system: lignin + 500 ozone + 3500 water for 1 ns and 0K starting temperature, Hi Lammps users, I’m trying to simulate the reaction between CaO and CO2 using reaxff. lammps. This could be useful for listing a large number of simulation parameters or input script names or random numbers or timestep values in the file and processing them, one at a time, Dear LAMMPS users and developers, I want to obtain the specific heat by calculating dH/dT under NPT ensemble. If the deform/normalize value is set to yes , then the When I am running this in lammps it shows the the E_pair, Total Energy and Pressure as NaN and terminates the program saying “Bad termination of one of your I dug into this and the problem is that pyiron. TIP3P water model — LAMMPS Highlight (see the Pictures and Movies pages for more examples of LAMMPS calculations) Blood flow in capillaries This is work by Kirill Lykov (kirill. This is a convenient way to evaluate a formula immediately without using the variable command to define a named variable and then This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. Post-Processing Requirements ! Lightweight " No fancy post-processing packages ! Extensible/Reusable " No obscure one-line commands ! General " No specialized LAMMPS commands ! Organized Workflow " Generate named files along the way . can you share a photo of LAMMPS log file Hello all, I am running molecular dynamics simulations in lammps and trying to calculate how polydispersity affects the pressure. 42996 -29802. In any case, no nans should arise in its position. I am encountering some negative pressure results during my simulation. Optionally, users may specify the relative amounts of different MC moves using the mcmoves keyword. control. 383859 1804. you ID, group-ID are documented in fix command. This command can only be used when fix nvt/uef or fix npt/uef is active. No global or per-atom quantities are stored by this fix for access by various output commands. Set-up: moving sphere impacting a fixed shere; contact model is pair_coeff * * dmt ${E} ${e_rest} ${nu} ${g_dmt} tangential mindlin NULL ${x_t} ${mu_s} rolling none twisting none damping coeff_restitution; Using the recently added damping mode 'coeff_restitution' with the DMT cohesion, this can result in nan positions of the moving sphere LAMMPS LAMMPS Mailing List Mirror. Thanks, Ly Le, Univ of Utah in. In its original implementation GD was used to compute the pressure required to achieve a fixed mass flux through an opening. 02273383910695e+00 3. 0-13-generic #22-Ubuntu SMP Wed Nov 2 13: one or more keyword/value pairs may be listed. The pair_style soft potential can be used to un-overlap atoms while running dynamics. LAMMPS (29 Sep 2021 - Update 1) relaxation for lattice constant P1 Initialization basic condition units metal #package omp 0 neigh yes # Nthreads=0 for default value set by OMP_NUM_THREADS environment dimension 3 #how MPI tasks are mapped to the simulation box processors * * * bo I am trying to simulate the Zinc oxide bulk structure (periodic) at constant pressure(0. 9412 1668. But it can be difficult to Dear All, I run a simulation and encounter following error: Non-numeric pressure - simulation unstable. meam file), pressure and forces cannot be calculated (-nan) see in the log file. I solved my problem by reconstructing the initial configuration. I would appreciate any advice Using LAMMPS you can calculate and print average pressure over window of some time, fluctuations of average pressure should be much smaller variable P equal press fix PressAve all ave/time 10 1000 In standard PIMD, the value used for a bead’s fictitious mass is arbitrary. Dear Team, I hope if you can help me with my problem and in all ways thank you for your enormous help in this mailing list. Temp=297, potential energy=0, total energy=519 while pressure, volume and density all becomes -nan. The fix_modify temp and press options are supported by this fix. LAMMPS certainly has global and local (atomic) measure of stress and pressure that can be calculated during a simulation. Added a file-style variable that allows it to read successive values (strings or numbers) from a file via the next command or the next() function in an equal-style or atom-style variable. I don’t know what’s wrong. In the last 2 examples, which will adjust the xy, xz, yz tilt factors to compensate for off-diagonal components of the pressure tensor. Probably pressure_to_lammps() needs to return a list with the None values All of the barostatting fixes use the compute pressure compute to calculate a current pressure. When using meam potential with cmin = 0. The formula for the components of the tensor is the same as the above expression for \(E_\mathrm{kin}\) , except that the 1/2 factor is NOT included and the \(v_i^2\) is replaced by \(v_{i,x} v_{i,y}\) for the \(xy\) 0 7800 300 nan -30104. Dear all, I want to get equilibrated lattice constants of crystal SiO2 at room temperature. After that I took the restart file and run NVT at 300K. The stress values will be in pressure units. As the GPU package generally provides the biggest speedup for my hardware, I'd like to get it working! LAMMPS Version and Platform. extremely high-pressure, high-density and/or high-temperature system. Fix that, and the minimization will likely proceed. A symmetric tensor, stored as a six-element vector, is I have changed different Pdamp value also and found that pressure varies from $\pu{-200 bar}$ to $\pu{+200 bar}$. I fixed T=300K. (for T = 280K and Hi all! I’m trying to calculate the pressure of a system composed by 60 atoms (20 molecules of CO2). 1. No parameter of this fix can be used with the start/stop keywords of the run command. As part of this, a new molecule command was added to LAMMPS, to allow specification of template molecules. I just want to know is the pressure is base on “absolute” or “gauge” pressure ? Just curious if negative pressure is acceptable or it is just a diverging solution. wall/piston = style name of this fix command. 2: 415: March 31, 2021 [lammps-users] Molecular dynamics simulation for all. If I run the simulations (in LJ units) with a size of 1 and a volume fraction of 30%, I 3 Dec 2012. If I run the simulations (in LJ units) with a size of 1 and a volume fraction of 30%, I A symmetric tensor, stored as a six-element vector, is also calculated by this compute for use in the computation of a pressure tensor by the compute pressue command. I face this problem. So, I am using this command fix 1 all press/berendsen iso 1 1 1000 fix 2 all nvt temp 300 300 100 but in output, I Note. 5 (in the Si_test. See the Build package page for more info. Run MD with LAMMPS 9. This fix writes the state of the Nose/Hoover barostat to binary restart files. It works fine. 本帖最后由 pumpkin111 于 2024-9-25 10:15 编辑 我用lammps做热解模拟，用的势文件是laspnn，体系只有CHO三种元素。因为不能用fix reaxff/species命令但是想得到species文件，所以想循环每一帧轨迹文件用reaxff做一个非常小小的模拟过程，来输出产物文件。 ERROR: Non-numeric pressure - simulation unstable (/fix_npt_cauchy. Jian-Hui_Zhai August 31, 2017, 2:59pm 1. saddle splay modulus. The density is 0. lj is not supported. physics. After the full relaxation, how to calculate the pressure of gas in the container under -30 degree centigrade? Is it possible to do the pressure statistic with molecular dynamic simulation; such as LAMMPS? Would anyone please give me some suggestions? Thank you in Dear all LAMMPS users, I am trying to simulate the compression test of the Al75Pd25 alloy. glycerol (4. 491 0 0 15. 383859 15. Best wishes, Xiaohui Dear all, I’m a (very) beginner in using LAMMPS. where KE = is the total kinetic energy of the group of atoms (sum of \(\frac12 m v^2\)), dim = 2 or 3 is the dimensionality of the simulation, \(N\) is the number of atoms in both the group and region, \(k_B\) is the Boltzmann constant, and \(T\) temperature. I use FeNiCr. The specified group must be “all”. Fixed a bug with an uninitialed normalization variable in thermo output that could be an issue when variables are evaluated before thermo output is ever performed. （持续更新，觉得有用就点个赞吧） 报错的代码各有各的错误，成功的代码却往往一模一样。 此贴用来记录自己一路上学lammps遇到的各种报错。 1. Simulation is goes well in other data. It’s good be great if you could help me to solve the problem. For the definition of kcal in real units, LAMMPS uses the thermochemical calorie = 4. Howe ID, group-ID are documented in fix command. 00 7. 723 204. 在1月14-20日期间，本论坛仅限等级≥level 4的成员发贴，带来的不便请谅解！其他成员若有学术问题请等到能发贴的时候再发帖。 This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. We also tried to add the compute temp in If you wish to insert molecules via the mol keyword, that will have their bonds or angles constrained via SHAKE, use the shake keyword, specifying as its value the ID of a separate fix shake command which also appears in your input script. Reporting bugs. I am getting some questionable values for pressure. alloy potential and read the model from a input file. ID, group-ID are documented in fix command. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is “all” since pressure is computed for the entire system. LAMMPS (22 Dec 2022) [packages EXTRA-*, GPU, KOKKOS, KSPACE, MOLECULE, OPT] When I am running this in lammps it shows the the E_pair, Total Energy and Pressure as NaN and terminates the program saying “Bad termination of one of your application process”. NOTE 1: The local stress does not include any Lennard-Jones tail corrections to the stress added by the pair_modify tail yes command, since those are contributions to the global system pressure. if energy/pressure are too high or infinity or NaN, then you probably have overlapping atom positions or Using LAMMPS you can calculate and print average pressure over window of some time, fluctuations of average pressure should be much smaller variable P equal press fix PressAve all ave/time 10 1000 Restart, fix_modify, output, run start/stop, minimize info . LammpsControl. However, I got lots of “nan” in the output when running NVT and could not explain why. goldnp_hexan_nonbond_reax in. Apply an external pressure or stress tensor to the simulation box during an energy minimization. Dear All, I want to calculate the permeability of some small gases on a membrane. While running for NVE simulation on the following system: lignin + 500 ozone + 3500 water for 1 ns and 0K starting temperature, 9. These values can be used by any command that uses global scalar or vector values from a compute as input. I convert eV to Respected peers, I am trying to simulate the lignin molecule with a mixture of ozone and water with reaxff potential (I used the reaxff potential available on the LAMMPS example. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. Develop branch, commit dad0d26 on Ubuntu 22. Dear lammps users, I would like to simulate point defects in YSZ, Volume 0 246. Not specifying the number in this case will cause the compute to fail. 0: 743: June 5, 2022 [lammps-users] Calculation of Respected peers, I am trying to simulate the lignin molecule with a mixture of ozone and water with reaxff potential (I used the reaxff potential available on the LAMMPS example. I wonder if you could give me some Considering the negative pressure, I incremented water molecules to 5000 but the pressure trend remained the same (I simulated this particular system for 10 ns). This can be used when a comb potential is used as part of the hybrid pair style. Define a computation that calculates the potential energy of the entire system of atoms. I have tried checking out the latest version of LAMMPS and the problem persists. Short problem description: I am trying to equilibrate the pressure to 1 atm in the direction perpendicular to the electrodes in an electrochemical cell, however I don’t understand how to interpret the much lower pressure that LAMMPS reports with the thermo output. The data is stored as local data so it can be accessed by other output commands that process local data, such as the compute reduce or dump local commands. The colliding sphere should bounce away or stay stuck, depending on the cohesion force intensity. calc_md() in line 516, there is a check if value is not None:, which will evaluate to True for nan. theory. 1 iso 0. ERROR on proc 1: Non-numeric atom coords - simulation unstable, I noticed the press showing as -nan, this may be the reason but I do not know how to fix it. Dear LAMMPS users and developers, I want to obtain the specific heat by calculating dH/dT under NPT ensemble. Or dynamics can be run using fix viscous to impose a damping force that slowly drains all kinetic energy from the system. , Jung, (files in. Dear LAMMPS list readers, I am new to LAMMPS and need some guidance in setting up my atomistic simulations. Questions: 1. Excuse I want to simulate a system that contain mW water with Sw potential and also hybrid with lj potential with other type particle everything is ok when I just use mpi run this system but when i try to use gpu to accelerate, the thermal output like pressure, get nan and finally system get crash. Dear LAMMPS developers and users, Greetings! We are calculating the pressure of a group of water by using the commands “compute pressure” and “compute stress/atom”. Hey All, I am writing to clear a doubt regarding NPT and NVT simulation in lammps, which is as follows: I take an initial configuration of randomly packed water molecules (TIP4P/Ice) in a certain volume. bending modulus. Thus you must use a separate time integration fix, like fix nve or fix nvt to actually update the positions and velocities of atoms. Attached please I have a small LAMMPS code which does tensile loading using displacement control on it. A Berendsen barostat will not work well for arbitrary values of Pdamp. I have also tried to use press/berendsen and temp/rescale with the SPE/E benchmark provided on the LAMMPS website with no success. Hi @alphataubio,. Note that the ID of this compute is thermo_press and the group is all. But at NVT the pressure goes down, remaining in equilibrium in 50 atm. Then, relax the gas system in this sealed container under -30 degree centigrade. At each iteration the force gradient is combined with the previous iteration information to compute a new search direction perpendicular (conjugate) to the previous search direction. 0: 743: June 5, 2022 [lammps-users] Calculation of 12. 6473 3640. The energy is calculated by the various pair, bond, etc. If you are confident that you have found a bug in LAMMPS, follow these steps. nist. eam. No information about this fix is written to binary restart files. If I run under The computed potential energy for the initial step is NaN (in particular the v_ew element) and the pressure tensor gets a NaN value. See this section for an overview of LAMMPS output options. keyword = psllod psllod value = no or yes = use SLLOD or p-SLLOD variant, respectively additional thermostat related keyword/value pairs from the fix nvt command can be appended. units . Examples LAMMPS LAMMPS Mailing List Mirror. See the discussion on the Howto 2d page for additional instructions on how to run 2d simulations. I know that this occurs due to the overlapping of I could make Lammps, and could create input script with a data file. 184 J. The anharmonic keyword will instruct the compute to return anharmonic properties rather than the full properties, which include lattice, harmonic and anharmonic contributions. 708120282 I have attached the input data and the code for relaxation. Can you please help me on this purpose? Stefan_Paquay October 14, 2018, 2:07am 2. For low values of g_dmt or large impact velocity, it bounces back properly. I’m now using addforce to the atom to mimic This command is used to compute the pressure tensor in the reference frame of the applied flow field when fix nvt/uef or fix npt/uef is used. due to using the npt integrator, this is detected and the simulation stopped immediately , as with the box update, all coordinates would become NaN and thus the simulation meaningless. After the full relaxation, how to calculate the pressure of gas in the container under -30 degree centigrade? Is it possible to do the pressure statistic with molecular dynamic simulation; such as LAMMPS? Would anyone please give me some suggestions? Thank you in Dear Sir, I am using press/berendsen barostat. However, no matter how I modify the model, the pressure always shows as nan during the minimization process. But when I change cmin to 0. Pressure formula for the flat Dear LAMMPS users, I am a novice user of the LAMMPS, currently trying to simulate the stretch of an elastoplastic system with initial crack using PERI package. 00 -3. 2. Description . I have run my simulation using ffield. ). However, note that Pdamp is specified in time units, and that timesteps are NOT the same as Restart, fix_modify, output, run start/stop, minimize info . This is typically due to a bad input geometry. A Nan pressure means forces are bad, likely infinite. This is unnecessary with the rerun command. However, the only methods to make the system converge on a target value of stress are use of the npX fixes (using periodic bc's) and the method I suggest. Note that this command only works with the fix you are confusing “internal” and “external” pressure and need to refresh your understanding of some basic physics. The translational kinetic energy is computed the same as is described by the compute temp command. 54. Respected peers, I am trying to simulate the lignin molecule with a mixture of ozone and water with reaxff potential (I used the reaxff potential available on the LAMMPS example. I am reading and studying other problems like this but can’t solve it properly or won’t understand the npt or nve issues. A good choice for many models is a Pdamp of around 1000 timesteps. 7638 -11900. How can I have an accurate char * LAMMPS_NS:: utils:: strdup (const std:: string & text) . if energy/pressure are too high or infinity or NaN, then you probably out the exact same version of LAMMPS from the svn repository on two different machines. See the compute pe/atom command if you want per-atom energies. cpp at develop · lammps/lammps Respected peers, I am trying to simulate the lignin molecule with a mixture of ozone and water with reaxff potential (I used the reaxff potential available on the LAMMPS example. This will eventually be used by other commands as well. it is missing the pressure control The specified pstyle must be a pair style used in your simulation either by itself or as a sub-style in a pair_style hybrid or hybrid/overlay command. the rest, i. Axel Kohlmeyer (Temple U_ made an upgrade to the USER-COLVARS package library and added a "purge" option to the master LAMMPS Makefile to assist in whacking obsolete files that may My model simulation is composed of a polymer-ion system including C/H/O/N/Li/S/F. 4532 3541. 0 1 Note. However, note that Pdamp is specified in time units, and that timesteps are NOT the same as However, when I run LAMMPS using the GPU package, the pressure is NaN (printout attached in Actual Behavior below). keyword = temp or iso or aniso or tri or x or y or z or xy or yz or xz or couple or tchain or pchain or mtk or tloop or ploop or nreset or drag or ptemp or dilate or scalexy or scaleyz or scalexz or flip or fixedpoint or update temp values = Tstart Tstop The values calculated by this compute are “intensive”. 5001, or replace one of the p boundary by s, or change Dear All, I want to calculate the permeability of some small gases on a membrane. 0 GPa) to observe phase transition with LAMMPS. The values Patomtrans, Public development project of the LAMMPS MD software package - lammps/src/compute_pressure. Dear All, I run a simulation and encounter following error: Non-numeric pressure - Hoping I can get help here. the values you get for energies and pressure will inform you whether your initial geometry is reasonable or invalid. Possible Solutions Dear professors, I am trying to simulate water, and it outputs "nan". 9888 g/cm^3. spontaneous curvature. See the Howto output doc page for an overview of LAMMPS output options. This is typically due to invalid physics and numerics that your simulation is computing. Molecular. Choose a minimization algorithm to use when a minimize command is performed. But during my fix NVE pressure fluctuates from 9 to 2 atm. Thus, could anyone tell me how does lammps compute the pressure at the timesteps which are not a multiple of 10000, such as the 666th timestep? Besides, if I use fix ave/time to get the pressure, like: This fix command will take the average I am receiving a “non-numeric pressure” error, which is causing my simulation to become unstable, Hello everyone, I am reaching out for assistance with an issue I’ve encountered during my molecular dynamics Dear Sir, I am using press/berendsen barostat. 00000000000000e+00 -nan 1000300 3. P6: Implementation of the pressure profile calculation in spherical coordinates AIST / CREST-JST Takenobu Nakamura and Wataru Shinoda Fluid Membrane Elastic coefficients are obtained by the pressure profile. Make C-style copy of string in new storage. The number density values are in inverse volume units. In trying to diagnose the issue, I simulated water only in a box with the same input and forcefield file and the I had no Description . xaqiw jqnws kmhsj sneie wqtrpq oivdmc lynctoh vxso chxdxqg qpy