1 LAMMPS Short Manual

User Manual:

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LAMMPSSHORT MANUAL
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MSLAB for LAMMPS on MIGALE
Custom LAMMPS installation
CUSTOM LAMMPS JOB
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MSLAB custom installation
custom PIZZA.py on MIGALE
PIZZA.py custom installation
CUSTOM PIZZA TEST
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PIZZA with GUI
LAMMPSEXAMPLES
BEAD-SPRING POLYMER MELT FENE: Finite Extendible Nonlinear Elastic Model (here: 2880 beads, 2715 bonds)
BEAD-SPRING POLYMER MELT FENE: Finite Extendible Nonlinear Elastic Model (here: 2880 beads, 2715 bonds)
BEAD-SPRING POLYMER MELT
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ALL ATOM SIMULATIONEXAMPLE 1: CVFF (no warnings), shrink boundary conditions
ALL ATOM SIMULATIONEXAMPLE 2: CVFF (warnings), shrink boundary conditions
ALL ATOM SIMULATIONEXAMPLE 3: CFF (warnings), periodic boundary conditions, NPT
MISCELLANEOUS
LEARNING PYTHON
LEARNING PYTHON
LEARNING PYTHON
LEARNING MATLAB
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VISUALIZATION OF DUMP FILES
WIN2LINUX Solutions
WIN2LINUX Solutions
WIN2LINUX Solutions
MAKING LAMMPS
$PROJECT\make\lammps-31Jan08\src\MAKE\Makefile.g++_lam_all_100208
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MODMOL25‐27Feb 2008,Jouy‐en‐Josas

olivier.vitrac@agroparistech.fr

Thisdocumentgathersseveralfreelyavailablesources.

Theresultisfreelydistributablewithoutguaranteeorwarranteeofanykind.

LAMMPS

LARGE

SCALE

ATOMIC

MOLECULAR

MASSIVELY

PARALLEL

SIMULATOR

INIT

ATOMDEFINITION

FORCEFIELDS

SETTINGS

FIX

COMPUTE

ACTIONS

OUTPUTS

LAMMPS is a molecular dynamics program from Sandia National

Laboratories. LAMMPS makes use of MPI for parallel communication and is a

free open‐source code, distributed under the terms of the GNU General

Public License.

LAMMPS was originally developed under a Cooperative Research and Development Agreement

(CRADA) between two laboratories from United States Department of Energy and three other

laboratories from private sector firms. It is currently maintained and distributed by researchers at the

Sandia National Laboratories.

For computational efficiency LAMMPS uses neighbor lists to keep track of nearby particles. The lists

are optimized for systems with particles that are repulsive at short distances, so that the local

density of particles never becomes too large.

On parallel computers, LAMMPS uses spatial‐decomposition techniques to partition the simulation

domain into small 3d sub‐domains, one of which is assigned to each processor. Processors

communicate and store "ghost" atom information for atoms that border their sub‐domain.

LAMMPS is most efficient (in a parallel computing sense) for systems whose particles fill a 3D

rectangular box with approximately uniform density.

Features

http://lammps.sandia.gov/

http://lammps.sandia.gov/doc/Manual.html 2

PRINCIPLES

1)Initialization

2)Atom definition

3)Settings

4)Run

units,dimension,boundary,atom_style,atom_modify.

read_data,read_restart,lattice,region,create_box,create_atoms

pair_coeff,bond_coeff,angle_coeff,dihedral_coeff,improper_coeff,

kspace_style,dielectric,special_bonds

neighbor,neigh_modify,group,timestep,reset_timestep,run_style,

min_style,min_modify.

compute,compute_modify,variable

run,minimize

SCRIPT

1)Initialization

2)Atom definition

3)Settings

4)Run

#3dLennard‐Jonesmelt

units lj

atom_style atomic

lattice fcc 0.8442

region boxblock020020020

create_box 1box

create_atoms 1

mass 11.0

velocity allcreate3.087287

pair_style lj/cut 2.5

pair_coeff 111.01.02.5

neighbor 0.3bin

neigh_modify every20delay0checkno

fix 1allnve

dump idallatom 10dump.melt

thermo 50

run 250 4

INIT

atom_modify

ATOM_STYLE

boundary

dimension

newton

processors

units

atom_style styleargs

angle =bondsandangles‐ e.g.bead‐spring polymers with stiffness

atomic =only thedefaultvalues

bond =bonds‐ e.g.bead‐spring polymers

charge =charge

dipole =chargeanddipole moment

dpd =defaultvalues,also communicates velocities

ellipsoid =quaternionforparticle orientation,angular velocity/momentum

full =molecular +charge‐ e.g.biomolecules,charged polymers

granular =granular atoms with rotational properties

molecular =bonds,angles,dihedrals,impropers ‐e.g.all‐atom polymers

INIT

atom_modify

atom_style

BOUNDARY

dimension

newton

processors

units

boundary xyz

x,y,z =porsorform,oneortwoletters

pisperiodic

fisnon‐periodicandfixed

sisnon‐periodicandshrink‐wrapped

misnon‐periodicandshrink‐wrapped

withaminimumvalue

INIT

atom_modify

atom_style

boundary

dimension

newton

processors

UNITS

units lj stylereal

distance=sigma

time=tau

mass=one

energy =epsilon

velocity =sigma/tau

force=epsilon/sigma

temperature =reduced LJ

temperature

pressure=reduced LJpressure

charge=reduced LJcharge

dipole =reduced LJdipole

moment

electric field =force/charge

distance=Angstroms

time=femtoseconds

mass=grams/mole

energy =Kcal/mole

velocity =Angstroms/femtosecond

force=Kcal/mole‐Angstrom

temperature =degrees K

pressure=atmospheres

charge=multipleofelectron

charge(+1.0is aproton)

dipole =charge*Angstroms

electric field =volts/Angstrom

ATOMDEFINITION

create_atoms

create_box

lattice

READ_DATA

read_restart

region

replicate

read_data file

atoms =#ofatoms insystem

bonds =#ofbondsinsystem

angles =#ofanglesinsystem

dihedrals =#ofdihedrals insystem

impropers =#ofimpropers insystem

atom types =#ofatom typesinsystem

bondtypes =#ofbondtypesinsystem

angletypes =#ofangletypesinsystem

dihedral types =#ofdihedral typesinsystem

improper types =#ofimproper typesinsystem

xlo xhi =simulationboxboundaries inxdimension

ylo yhi =simulationboxboundaries inydimension

zlo zhi =simulationboxboundaries inzdimension

xy xz yz =simulationboxtiltfactors fortriclinic domain 8

ATOMDEFINITION

create_atoms

create_box

lattice

READ_DATA

read_restart

region

replicate

LAMMPS Description (1st line of file)

100 atoms (this must be the 3rd line, 1st 2 lines are ignored)

95 bonds (# of bonds to be simulated)

50 angles (include these lines even if number = 0)

30 dihedrals

20 impropers

5 atom types (# of nonbond atom types)

10 bond types (# of bond types = sets of bond coefficients)

18 angle types

20 dihedral types (do not include a bond, angle,dihedral,improper type

2 improper types line if number of bonds,angles,etc is 0)

-0.5 0.5 xlo xhi (for periodic systems this is box size,

-0.5 0.5 ylo yhi for non-periodic it is min/max extent of atoms)

-0.5 0.5 zlo zhi (do not include this line for 2-d simulations)

Masses

1 mass

...

N mass (N = # of atom types)

Pair Coeffs Nonbond Coeffs (in old versions)

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of atom types)

Bond Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of bond types)

Angle Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of angle types) 9

ATOMDEFINITION

create_atoms

create_box

lattice

READ_DATA

read_restart

region

replicate

Dihedral Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of dihedral types)

Improper Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of improper types)

BondBond Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of angle types)

BondAngle Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of angle types)

MiddleBondTorsion Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of dihedral types)

EndBondTorsion Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of dihedral types)

AngleTorsion Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of dihedral types) 10

ATOMDEFINITION

create_atoms

create_box

lattice

READ_DATA

read_restart

region

replicate

AngleAngleTorsion Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of dihedral types)

BondBond13 Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of dihedral types)

AngleAngle Coeffs

1 coeff1 coeff2 ...

...

N coeff1 coeff2 ... (N = # of improper types)

Atoms

1 molecule-tag atom-type q x y z nx ny nz (nx,ny,nz are optional -

... see "true flag" input command)

...

N molecule-tag atom-type q x y z nx ny nz (N = # of atoms)

Velocities

1 vx vy vz

...

N vx vy vz (N = # of atoms)

Bonds

1 bond-type atom-1 atom-2

...

N bond-type atom-1 atom-2 (N = # of bonds)

Angles

1 angle-type atom-1 atom-2 atom-3 (atom-2 is the center atom in angle)

...

N angle-type atom-1 atom-2 atom-3 (N = # of angles) 11

ATOMDEFINITION

create_atoms

create_box

lattice

READ_DATA

read_restart

region

replicate

Dihedrals

1 dihedral-type atom-1 atom-2 atom-3 atom-4 (atoms 2-3 form central bond)

...

N dihedral-type atom-1 atom-2 atom-3 atom-4 (N = # of dihedrals)

Impropers

1 improper-type atom-1 atom-2 atom-3 atom-4 (atom-2 is central atom)

...

N improper-type atom-1 atom-2 atom-3 atom-4 (N = # of impropers)

comments

blank lines are ignored

lines starting with a # are echoed into the log file

for commands, everything on a line after the last

parameter is ignored

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

pair_style

pair_write

special_bonds 13

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

pair_style

pair_write

special_bonds

The presence of cross terms in a force field reflects coupling between

the internal coordinates. For example, as a bond angle is decreased it

is found that the adjacent bonds stretch to reduce the interaction

between the 1,3 atoms, as illustrated in Figure. Cross terms were

found to be important in force fields designed to predict vibrational

spectra that were the forerunners of molecular mechanics force

fields, and so it is not surprising that cross terms must often be

included in a molecular mechanics force field to achieve optimal

performance.

One should in principle include cross terms between all contributions

to a force field. However, only a few cross terms are generally found

to be necessary in order to reproduce structural properties accurately;

more may be needed to reproduce other properties such as

vibrational frequencies, which are more sensitive to the presence of

such terms,.

Crossterms:class1,2and3forcefields

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

pair_style

pair_write

special_bonds

TYPEI:CVFF(CovalentFF)

TYPEII:CFF

(ConsistentFF)

FORCEFIELD

angle_coeff

ANGLE_STYLE

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

pair_style

pair_write

special_bonds

angle_style none ‐turn offangleinteractions

angle_style hybrid ‐define multiplestylesofangleinteractions

angle_style charmm ‐CHARMMangle

angle_style class2 ‐COMPASS(class2)angle

angle_style cosine ‐cosine anglepotential

angle_style cosine/delta ‐difference ofcosines anglepotential

angle_style cosine/squared ‐cosine squared anglepotential

angle_style harmonic ‐harmonic angle

style Expression Examples

harmonic K(energy/radian^2)

theta0(degrees)

angle_style harmonic

angle_coeff 1300.0107.0

Charmm K(energy/radian^2)

theta0(degrees)

K_ub (energy/distance^2)

r_ub (distance)

angle_style charmm

angle_coeff 1300.0107.050.03.0

class2 angle_style class2

angle_coeff *75.0

()

=−

()()()

()( )

()

234

203040

11 02 2 0

abbba

bb ij jk

ba ij jk

EE E E

EK K K

EMr rr r

ENrr Nrr

θθ θθ θθ

θθθ

=−+−+−

−−

=−−+ −−

() ( )

0UB UB

EK K rr

θθ

=−+ −

FORCEFIELD

angle_coeff

angle_style

bond_coeff

BOND_STYLE

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

pair_style

pair_write

special_bonds

style Expression Examples

harmonic K(energy/distance^2)

r0(distance)

bond_style harmonic

bond_coeff 580.01.2

class2 r0(distance)

K2(energy/distance^2)

K3(energy/distance^2)

K4(energy/distance^2)

bond_style class2

bond_coeff 11.0100.080.080.0

()

EKrr=−

bond_style none ‐turn offbonded interactions

bond_style hybrid ‐define multiplestylesofbondinteractions

bond_style class2 ‐COMPASS(class2)bond

bond_style fene ‐FENE(finite‐extensiblenon‐linear elastic)bond

bond_style fene/expand ‐FENEbondswith variablesizeparticles

bond_style harmonic ‐harmonic bond

bond_style morse ‐Morsebond

bond_style nonlinear ‐nonlinear bond

bond_style quartic ‐breakable quartic bond

() () ()

234

20 30 40

Krr Krr Krr=−+−+−

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

DIHEDRAL_STYLE

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

pair_style

pair_write

special_bonds

dihedral_style none ‐turn offdihedral interactions

dihedral_style hybrid ‐define multiplestylesofdihedral interactions

dihedral_style charmm ‐CHARMMdihedral

dihedral_style class2 ‐COMPASS(class2)dihedral

dihedral_style harmonic ‐harmonic dihedral

dihedral_style helix ‐helix dihedral

dihedral_style multi/harmonic ‐multi‐harmonic dihedral

dihedral_style opls ‐OPLSdihedral

style Expression Examples

harmonic K(energy)

d(+1or‐1)

n(integer >=0)

dihedral_style harmonic

dihedral_coeff 180.012

Charmm K(energy)

n(integer>=0)

d(integervalueofdegrees)

weightingfactor(0.0to1.0)

dihedral_style charmm

dihedral_coeff 1120.01600.5

class2 dihedral_style class2

dihedral_coeff 110075100708060

()

1cosEK d n

⋅+⋅ ⋅

⎡

⎤

⎣

⎦

(

)

1cosEK n d

=⋅+ ⋅−

⎡

⎤

⎣

⎦

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

IMPROPER_STYLE

kspace_modify

kspace_style

pair_coeff

pair_modify

pair_style

pair_write

special_bonds

improper_style none ‐turn offimproper interactions

improper_style hybrid ‐define multiplestylesofimproper interactions

improper_style class2 ‐COMPASS(class2)improper

improper_style cvff ‐CVFFimproper

improper_style harmonic ‐harmonic improper

style Expression Examples

harmonic K(energy/radian^2)

X0(degrees)

improper_style harmonic

improper_coeff 1100.00

CVFF K(energy)

d(+1or‐1)

n(0,1,2,3,4,6)

improper_stylecvff

improper_coeff180.0‐14

class2 improper_style class2

improper_coeff 1100.00

()

=−

(

)

1cosEK d n

⋅+⋅ ⋅

⎡

⎤

⎣

⎦

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

PAIR_STYLE

pair_write

special_bonds

pair_style lj/charmm/coul/charmm ‐CHARMMpotential with cutoff Coulomb

pair_style lj/charmm/coul/charmm/implicit ‐CHARMMforimplicit solvent

pair_style lj/charmm/coul/long ‐CHARMMwith long‐rangeCoulomb

pair_style lj/charmm/coul/long/opt ‐optimized versionofCHARMMwith long‐rangeCoulomb

pair_style lj/class2 ‐COMPASS(class2)forcefield with noCoulomb

pair_style lj/class2/coul/cut ‐COMPASSwith cutoff Coulomb

pair_style lj/class2/coul/long ‐COMPASSwith long‐rangeCoulomb

pair_style lj/cut ‐cutoff Lennard‐Jonespotential with noCoulomb

pair_style lj/cut/opt ‐optimized versionofcutoff LJ

pair_style lj/cut/coul/cut ‐LJwith cutoff Coulomb

pair_style lj/cut/coul/debye ‐LJwith Debyescreeningadded toCoulomb

pair_style lj/cut/coul/long ‐LJwith long‐rangeCoulomb

pair_style lj/cut/coul/long/tip4p ‐LJwith long‐rangeCoulombforTIP4Pwater

pair_style lj/expand ‐Lennard‐Jonesforvariablesizeparticles

pair_style lj/smooth ‐smoothed Lennard‐Jonespotential

Van‐der‐Waals with

Lorentz—Berthelot mixing rule

12 6

av.diameter 2

av.welldepth

ij ij

ii ij

ij ii ij

Err

σσ

εε

⎡

⎤

⎛⎞⎛⎞

⎢

⎥

=−

⎜⎟⎜⎟

⎢

⎥

⎝⎠⎝⎠

⎣

⎦

Coulomb

12 2 1 2

8.8542·10 C N m

1 for a vacuum by definition

Rij

πε ε

−−−

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

PAIR_STYLE

pair_write

special_bonds

pair_style hybrid ‐multiplestylesofpairwise interactions

pair_style hybrid/overlay ‐multiplestylesofsuperposed pairwise interactions

pair_style airebo ‐AI‐REBOpotential

pair_style buck ‐Buckinghampotential

pair_style buck/coul/cut ‐Buckinghamwith cutoff Coulomb

pair_style buck/coul/long ‐Buckinghamwith long‐rangeCoulomb

pair_style colloid ‐integrated colloidal potential

pair_style coul/cut ‐cutoff Coulombic potential

pair_style coul/debye ‐cutoff Coulombic potential with Debyescreening

pair_style coul/long ‐long‐rangeCoulombic potential

pair_style dipole/cut ‐pointdipoles with cutoff

pair_style dpd ‐dissipativeparticle dynamics (DPD)

pair_style eam ‐embedded atom method (EAM)

pair_style eam/opt ‐optimized versionofEAM

pair_style eam/alloy ‐alloy EAM

pair_style eam/alloy/opt ‐optimized versionofalloy EAM

pair_style eam/fs ‐Finnis‐SinclairEAM

pair_style eam/fs/opt ‐optimized versionofFinnis‐SinclairEAM

pair_style gayberne ‐Gay‐Berneellipsoidal potential

pair_style gran/hertzian ‐granular potential with Hertizain interactions

pair_style gran/history ‐granular potential with history effects

pair_style gran/no_history ‐granular potential without history effects

pair_style lubricate ‐hydrodynamic lubrication forces

pair_style meam ‐modified embedded atom method (MEAM)

pair_style morse ‐Morsepotential

pair_style morse/opt ‐optimized versionofMorsepotential

pair_style resquared ‐Everaers RE‐Squared ellipsoidal potential

pair_style soft ‐Soft(cosine)potential

pair_style sw ‐Stillinger‐Weber3‐bodypotential

pair_style table ‐tabulated pairpotential

pair_style tersoff ‐Tersoff 3‐bodypotential

pair_style yukawa ‐Yukawa potential

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

PAIR_STYLE

pair_write

special_bonds

style Expression Examples

lj/cut pair_style lj/cut2.5

pair_coeff 1111.12.8

lj/cut/coul

/cut

pair_style lj/cut/coul/cut10.08.0

pair_coeff 11100.03.59.0

lj/class2 pair_style lj/class210.0

pair_coeff 11100.03.59.0

lj/class2/c

oul/cut

pair_style lj/class2/coul/cut

10.08.0

pair_coeff 11100.03.59.0

12 6

vdw C

EE rr

σσ

⎡⎤

⎛⎞ ⎛⎞

=−<

⎢⎥

⎜⎟ ⎜⎟

⎝⎠ ⎝⎠

⎢⎥

⎣⎦

vdw C

EC rr

for

vdw

EE rr

σσ

⎡

⎤

⎛⎞ ⎛⎞

== −

⎢

⎥

⎜⎟ ⎜⎟

⎝⎠ ⎝⎠

⎢

⎥

⎣

⎦

for

vdw

EE Cr

epsilon(energy units)

sigma(distanceunits)

cutoff (distanceunits)

cutoff2(distanceunits)

FORCEFIELD

angle_coeff

angle_style

bond_coeff

bond_style

dielectric

dihedral_coeff

dihedral_style

improper_coeff

improper_style

kspace_modify

kspace_style

pair_coeff

pair_modify

pair_style

pair_write

special_bonds

pair coeff 1 2 1.0 3.45 10.0 (pair style lj/cutoff)

pair coeff 1 2 1.0 3.45 8.0 10.0 (pair style lj/smooth)

pair coeff 1 2 1.0 3.45 2.0 10.0 (pair style lj/shift)

pair coeff 1 2 1.0 30.0 2.5 (pair style soft)

pair coeff 1 2 1.0 3.45 10.0 (pair style class2/cutoff)

pair coeff 1 2 1.0 3.45 1.0 3.45 (pair style lj/charmm)

pair coeff 1 2 1.0 3.45 12.0 10.0 (pair style expo_6/cutoff)

pair coeff 1 2 1.0 3.45 12.0 10.0 12. 0 (pair style expo_6/spline)

pair coeff 1 2 1.0 3.45 12.0 10.0 (pair style expo_6/smooth)

special bonds amber

special bonds 0.0 0.0 0.5

pppm mesh 32 32 64

pppm order 5

dielectric 1

angle coeff 1 30.0 108.0 (angle style harmonic)

angle coeff 1 30.0 108.0 30.0 2.5 (angle style charmm)

angle coeff 1 30.0 108.0 (angle style cosharmonic)

bond coeff 1 100.0 3.45 (bond style harmonic)

bond coeff 1 30.0 1.5 1.0 1.0 (bond style fene/standard )

bond coeff 1 30.0 1.5 1.0 1.0 0.2 (bond style fene/shift)

bond coeff 1 28.0 0.748308 0.166667 (bond style nonlinear)

dihedral coeff 1 10.0 1 3 (dihedral style harmonic)

dihedral coeff 1 2.0 2.0 2.0 2.0 2.0 (dihedral style multiharmonic)

dihedral coeff 1 2.0 5 180.0 0.5 (dihedral style charmm)

dihedral coeff 1 2.0 1 3.0 (dihedral style dreiding)

improper coeff 1 20.0 0.0 (improper style harmonic)

improper coeff 1 20.0 10.0 (improper style cvff)

EXAMPLES

(whenused,mustappearafter"readdata"or"readrestart"command)

SETTINGS

communicate

dipole

group

mass

min_modify

min_style

neigh_modify

NEIGHBOR

reset_timestep

run_style

set

shape

timestep

velocity

neighbor skinstyle

neighbor0.3bin

neighbor2.0nsq

This command sets parameters that affect the building of the

pairwise neighbor list. All atom pairs within a cutoff distance equal

tothetheirforcecutoffplustheskin distance are stored in the list.

Typically, the larger the skin distance, the less often neighbor lists

need to be built, but more pairs must be checked for possible force

interactions every timestep. 24

FIX

fix

fix_modify

unfix

ˆobs

obs

∑

FIX

fix_modify

unfix

fix idallnve

nve ‐constantNVEtimeintegration

nve/asphere ‐NVTforaspherical particles

nve/dipole ‐NVEforpointdipolarparticles

nve/gran ‐NVEforgranularparticles

nve/limit ‐NVEwithlimitedsteplength

nve/noforce ‐NVEwithoutforces(vonly)

nvt ‐constantNVTtimeintegrationviaNose/Hoover

nvt/asphere ‐NVTforaspherical particles

nvt/sllod ‐NVTforNEMDwithSLLODequations

npt ‐constantNPTtimeintegrationviaNose/Hoover

npt/asphere ‐NPTforaspherical particles

fix idallnvt

fix idallnpt

fix IDgroup‐IDnpt Tstart Tstop Tdamp p‐styleargs keywordvalue...

xyz args =Pstart Pstop Pdamp

Pstart,Pstop =desiredpressureatstart/endofrun(pressureunits)

Pdamp =pressuredampingparameter(timeunits)

xy oryz orxz oraniso args =Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp

Px_start,Px_stop,...=desiredpressureinx,y,z atstart/endofrun(pressureunits)

Pdamp =pressuredampingparameter(timeunits)

fix IDgroup‐IDnvt Tstart Tstop Tdamp keywordvalue...

ID,group‐IDaredocumentedinfix command

nvt =stylenameofthisfixcommand

Tstart,Tstop =desiredtemperatureatstart/endofrun

Tdamp =temperaturedampingparameter(timeunits)

zeroormorekeyword/valuepairsmaybeappended

keyword=drag

fix IDgroup‐IDnve

ID,group‐IDaredocumentedinfix command

nve =stylenameofthisfixcommand

FIX

fix_modify

unfix

fix IDgroup‐IDstyleargs

addforce ‐addaforcetoeachatom

aveforce ‐addanaveragedforcetoeachatom

ave/atom ‐computeper‐atomtime‐averagedquantities

ave/spatial ‐outputper‐atomquantitiesbylayer

ave/time ‐outputtime‐averagedcomputequantities

com ‐computeacenter‐of‐mass

coord/original ‐storeoriginalcoords ofeachatom

deform ‐changethesimulationboxsize/shape

deposit ‐addnewatomsaboveasurface

drag ‐dragatomstowardsadefinedcoordinate

dt/reset ‐resetthetimestep basedonvelocity,forces

efield ‐imposeelectricfieldonsystem

enforce2d ‐zerooutz‐dimensionvelocityandforce

freeze ‐freezeatomsinagranularsimulation

gravity ‐addgravitytoatomsinagranularsimulation

gyration ‐computeradiusofgyration

heat ‐add/subtractmomentum‐conservingheat

indent ‐imposeforceduetoanindenter

langevin ‐Langevin temperaturecontrol

lineforce ‐constrainatomstomoveinaline

msd ‐computemean‐squareddisplacement(i.e.diffusion

coefficient)

momentum ‐zerothelinearand/orangularmomentumof

agroupofatoms

nph ‐constantNPHtimeintegrationviaNose/Hoover

npt ‐constantNPTtimeintegrationviaNose/Hoover

npt/asphere ‐NPTforaspherical particles

nve ‐constantNVEtimeintegration

nve/asphere ‐NVTforaspherical particles

nve/dipole ‐NVEforpointdipolarparticles

nve/gran ‐NVEforgranularparticles

nve/limit ‐NVEwithlimitedsteplength

nve/noforce ‐NVEwithoutforces(vonly)

nvt ‐constantNVTtimeintegrationviaNose/Hoover

nvt/asphere ‐NVTforaspherical particles

nvt/sllod ‐NVTforNEMDwithSLLODequations

orient/fcc ‐addgrainboundarymigrationforce

planeforce ‐constrainatomstomoveinaplane

poems ‐constrainclustersofatomstomoveas

coupledrigidbodies

pour ‐pournewatomsintoagranularsimulation

domain

print ‐printtextandvariablesduringasimulation

rdf ‐computeradialdistributionfunctions

recenter ‐constrainthecenter‐of‐masspositionofa

groupofatoms

rigid ‐constrainoneormoreclustersofatomsto

moveasarigidbody

setforce ‐settheforceoneachatom

shake ‐SHAKEconstraintsonbondsand/orangles

spring ‐applyharmonicspringforcetogroupofatoms

spring/rg ‐springonradiusofgyrationofgroupof

atoms

spring/self ‐springfromeachatomtoitsorigin

temp/rescale ‐temperaturecontrolbyvelocity

rescaling

tmd ‐guideagroupofatomstoanewconfiguration

viscosity ‐Muller‐Plathe momentumexchangefor

viscositycalculation

viscous ‐viscousdampingforgranularsimulations

wall/gran ‐frictionalwall(s)forgranularsimulations

wall/lj126 ‐Lennard‐Jones12‐6wall

wall/lj93 ‐Lennard‐Jones9‐3wall

wall/reflect ‐reflectingwall(s)

wiggle ‐oscillatewallsandfrozenatoms

FIX

fix

fix_modify

unfix assign fix 1atom 200

assign fix 1molecule 50

assignfix 1type2

assignfix 1region0.01.0INFINF0.01.0

assignfix 1bondtype 4

assignfix 1remainder

fix style none

fix style 1setforce 0.0NULL0.0

fix style 1addforce 1.00.00.0

fix style 1aveforce 1.00.00.0

fix style 1rescale300.0300.010020.00.5

fix style 1hoover/drag50.050.00.001

fix style 1langevin50.050.00.0112345111

fix style 1springforce 10.0NULLNULL 1.0

fix style 1dragforce 10.0‐5.0NULL2.01.0

fix style 1shake30.001100

EXAMPLESOFCONSTRAINTS

(whenused,mustappearafter"readdata"or"readrestart"command)

COMPUTES

COMPUTE

compute_modify

uncompute

centro/atom ‐centro‐symmetry parameter foreach atom

coord/atom ‐coordinationnumber foreach atom

displace/atom ‐displacement ofeach atom

group/group ‐energy/forcebetween two groupsofatoms

ke/atom ‐kinetic energy foreach atom

pe ‐potential energy

pe/atom ‐potential energy foreach atom

pressure ‐totalpressureandpressuretensor

reduce ‐combineper‐atom quantities into asingleglobalvalue

rotate/dipole ‐rotational energy ofdipolar atoms

rotate/gran ‐rotational energy ofgranular atoms

stress/atom ‐stresstensor foreach atom

temp ‐temperature ofgroupofatoms

temp/asphere ‐temperature ofaspherical particles

temp/deform ‐temperature excluding boxdeformation velocity

temp/dipole ‐temperature ofpointdipolar particles

temp/partial ‐temperature excluding oneormoredimensionsofvelocity

temp/ramp ‐temperature excluding ramped velocity component

temp/region ‐temperature ofaregion ofatoms

compute IDgroup‐IDstyleargs

compute1alltemp

computenewtemp flowtemp/partial110

compute3allke/atom

ACTIONS

delete_atoms

delete_bonds

displace_atoms

displace_box

minimize

RUN

temper

run Nkeywordvalues

N=#oftimesteps

zeroormorekeyword/valuepairsmaybeappended

keyword=upto orstart orstop orpre orpost orevery

run10000run1000000upto

run100start0stop1000

run1000prenopostyes

run100000start0stop1000000every1000print"ProteinRg =$r“

run100000every1000NULL

minimize tolerance maxiter maxeval

OUTPUT

DUMP

dump_modify

restart

thermo

thermo_modify

thermo_style

undump

write_restart

dump IDgroup‐IDstyleNfileargs

ID=user‐assignednameforthedump

group‐ID=IDofthegroupofatomstobedumped

style=atom orbond ordcd orxtc orxyz orcustom

N=dumpeverythismanytimesteps

file=nameoffiletowritedumpinfoto

args =listofargumentsforaparticularstyle

dumpmyDump allatom 100

dump.atom dump2subgroup atom 50

dump.run.bindump4aallcustom100

dump1allxtc 1000file.xtc

OUTPUT

dump

dump_modify

restart

THERMO

thermo_modify

thermo_style

undump

write_restart

thermo_style styleargs

style=one ormulti orgranular orcustom

args =listofargumentsforaparticularstyle

one args = none

multi args = none

granular args = none

custom args = list of attributes

possible attributes = step, atoms, cpu, temp, press,

pe, ke, etotal, enthalpy,

evdwl, ecoul, epair, ebond, eangle, edihed, eimp,

emol, elong, etail,

vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,

pxx, pyy, pzz, pxy, pxz, pyz

drot, grot,

c_ID, c_ID[n], f_ID, f_ID[n], v_name

step = timestep

atoms = # of atoms

cpu = elapsed CPU time

temp = temperature

press = pressure

pe = total potential energy

ke = kinetic energy

etotal = total energy (pe + ke)

enthalpy = enthalpy (pe + press*vol)

evdwl = VanderWaal pairwise energy

ecoul = Coulombic pairwise energy

epair = pairwise energy (evdwl + ecoul + elong + etail)

ebond = bond energy

eangle = angle energy

edihed = dihedral energy

eimp = improper energy

emol = molecular energy (ebond + eangle + edihed + eimp)

elong = long-range kspace energy

etail = VanderWaal energy long-range tail correction

vol = volume

lx,ly,lz = box lengths in x,y,z

xlo,xhi,ylo,yhi,zlo,zhi = box boundaries

pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor

drot = rotational energy of dipolar atoms

grot = rotational energy of granular atoms

c_ID = global scalar value calculated by a compute with ID

c_ID[N] = Nth component of global vector calculated by a compute with ID

f_ID = global scalar value calculated by a fix with ID

f_ID[N] = Nth component of global vector calculated by a fix with ID

v_name = global valuecalculatedbyanequal‐stylevariablewithname32

TOOLS DESCRIPTION

amber2lammps Pythonscriptsforconvertingfilesback‐and‐forthbetweentheAMBERMDcodeandLAMMPS

binary2txt convertsoneormorebinaryLAMMPSdumpfileintoASCIItextfiles

ch2lmp containstoolsforconvertingfilesback‐and‐forthbetweentheCHARMMMDcodeandLAMMPS

chain LAMMPSdatafilecontainingbead‐springpolymerchainsand/ormonomersolventatoms

data2xmovie convertsaLAMMPSdatafileintoasnapshotsuitableforvisualizingwiththexmovie tool

eam generate convertsananalyticformulaintoatabulatedembeddedatommethod(EAM) setfl potentialfile

lmp2arc convertingLAMMPSoutputfilestotheformatforAccelrys's InsightMDcode

lmp2cfg toolforconvertingLAMMPSoutputfilesintoaseriesof*.cfgfileswhichcanbereadintotheAtomEye

visualizer

lmp2traj toolforconvertingLAMMPSoutputfilesinto3analysisfiles

matlab /MSLAB severalMATLAB scriptsforpost‐processingLAMMPSoutput

micelle2d createsaLAMMPSdatafilecontainingshortlipidchainsinamonomersolution

msi2lmp toolforcreatingLAMMPSinputdatafilesfromAccelrys's InsightMDcode(formerlyMSI/Biosysm andits

DiscoverMDcode)

pymol_asphere toolforconvertingaLAMMPSdumpfilethatcontainsorientationinfoforellipsoidalparticlesintoaninput

fileforthePyMol visualizationpackage

restart2data convertsabinaryLAMMPSrestartfileintoanASCIIdatafile

thermo_extract readsoneofmoreLAMMPSlogfilesandextractsathermodynamicvalue(e.g.Temp,Press)

vim ,xmovie X‐basedvisualizationpackagethatcanreadLAMMPSdumpfilesandanimatethem 33

MODMOL25‐27Feb 2008,Jouy‐en‐Josas

olivier.vitrac@agroparistech.fr

Thisdocumentisbasedonourowncontribution.

Theresultisfreelydistributablewithoutguaranteeorwarranteeofanykind.

# MSLAB starts within $PROJECT

# example of line to be added/updated in ~/.bashrc

export PROJECT="~/project"

CustomLAMMPSinstallation

Important definitions for LAMMPS in this ./.bashrc (use LAMRC to see the related HELP)

Installation parameters

=======================

topaze: open a ssh connection on topaze

see also: GENKEY, EXPORTKEY (to make it possible a SSH connection without password on cluster

nodes)

$PROJECT: main directory of LAMMPS projects (TO BE CHECKED with "echo $PROJECT")

LAMMPS scripts must be located in $PROJECT (default) or in its subdirectories (e.g. examples)

LAMMPS jobs are automatically stored in $PROJECT/XXXXX (where X=[A-Z0-9])

see also: LSLAM, CDLAM, TREELAM

Included directories

bin/ LAMMPS executables (several versions are available)

executions with MPICH should be avoided, LAM/MPI must be preferred as it is

integrated with SUN GRID ENGINE

bin/tools/ other executables

doc/ documentation

make/ make directory (for advanced users)

examples/ examples

pizza/ PYTHON interface to LAMMPS (see PIZZA)

installation file has been modified to match $PROJECT

NB: PIZZA works on LINUX and WINDOWS XP/Vista

MSLAB (Matlab with the toolbox MS) requires:

> a directory $PROJECT/../codes/MS where all MS functions are located

> a script $PROJECT/startms.m where the GLOBAL variables LAMMPS and PATHPROJECT are defined

> The variable LAMMPS must be updated to your needs (e.g. define your e-mail).

NB: MSLAB works on LINUX and WINDOWS XP/Vista

FILE:~/.bashrc

CUSTOMLAMMPSJOB

Typical job $PROJECT/XXXXX

===========================

Each job directory contains initially:

a LAMMPS executable: e.g. lmp_g++_lam_all_100208 (last version 10/02/08 for LAM/MPI, including all

modules)

a LAMMPS input file: e.g. long.in.lj

additional data files: e.g. data.micelle (see LAMJOB to add user files)

3 shell scripts:

run.sh: submit the job on the cluster via SUN GRID ENGINE

manual queueue and execution on the cluster via: $PROJECT/XXXXX/run.sh (or ./run.sh)

lammpsscript.sh: (e.g. long.in.sh) main launcher via MPIRUN (can be used direclty on TOPAZE)

manual execution on TOPAZE via: $PROJECT/XXXXX/lammpsscript.sh (or ./lammpsscript.sh)

prior a manual execution on TOPAZE, an active lamboot is required and subsequently a

lamhalt (lamboot and lamhalt lines in the scrip are inactivated by default in the script

since they are managed automatically by the SUN GRID ENGINE)

mpi.sh: MPI argument (to used only by lammpsscript.sh)

After/during execution, several files are created:

jobid: jod id to be used with qstat -j jobid

project.log: log file

project.out: standard output (STDOUT)

project.err: standard error (STDERR)

lammps.log: additional log (default)

see also: MSLAB, PIZZA, RMLAMJOB, CLLAMJOB, LAMAN, TREELAM, PSSEARCH

FILE:~/.bashrc

BASHWRAPPERS DESCRIPTION USAGE

cdlam cd intoaLAMMPSdir/path cdlam localpath

cllamjob orcllammpsjob cleanLAMMPSjobsviaMSLAB ccllamjob jobname1[jobname2][jobname3][jobname4]...

exportkey exportRSAkeyonthecluster exportkey firstnode [lastnode]

genkey RSAgenkey (requireforSSH) genkey

killsearch killaprocessonallnodes killsearch processname [username][firs

msi2lmp convertaMSIprojectintoaLammps

data file msi2lmpmsiproject [class][ff][print][ffpath]

laman helponLAMMPSscriptcommand laman [lammps_command]

lamjob,lammpsjob Prepare/queue/runaLAMMPSjobvia

MSLABon thecluster

lamjob mylammpsscript cmd[numproc][jobname][jobpath]

[jobpath][datafile1][datafile2]…

cmd =run,scriptorrunone

lamrc orlammpsrc displayageneral helpvia.bashrc lamrc

lslam ls intoaLAMMPSdir/path lslam localpath

mslab matlab withMS(textmode) mslab,see"helpMS"fordetailedfunct

pizza PYTHONextensionforLAMMPS

(custominstallation) pizza

pssearch searchaprocessonallnodes pssearch processname [username][firstn

rmlamjob orrmlammpsjob remove LAMMPSjobsviaMSLAB rmlamjob jobname1[jobname2][jobname3][jobname4]...

treelam tree allLAMMPSprojects treelam,treelam long,treelam short

ulist alljobsforthecurrent user u

FILE:~/.bashrc

MSLAB FUNCTIONS DESCRIPTION

cllammpsjob cleanaorseveralLAMMPSjobs(removetheLAMMPSexecutable)

lamdumpread readLAMMPSdumpfile(allfieldsareidentifiedafterthekeyword'ITEM:'andthefollowing

valuesareassumedtobenumerical)

readlog LAMMPSlogfiles

lammpsjob createandlaunchaLAMMPSjobonthecluster(asdefinedinglobalvariables:PROJECTPATHand

LAMMPS)

lmp2cfg LAMMPSdumpfiletoExtendedCFGFormat(Novelocity)tobeused

msi2lmp convertsaMSIproject (MSIproject.car,MSIproject.mdf)intoaLAMMPSdatafile

readdump_all alltimesteps fromaLAMMPSdumpfile

readdump_one LAMMPSdumpfileonetimestep atatime

readlog LAMMPSlogfiles

readrdf toreadRadialDistributionFuntion outputfromLAMMPS

rmlammpsjob removeaorseveralLAMMPSjob(s)(deletetheentiredirectoriescreatedbyLAMMPSJOB)

scandump toscanLAMMPSdumpfile

MS(Molecular Studio)Toolbox forMatlab include 254functions

Maincontributor:O.Vitrac

LINUXCAPAPLE,WIN32/64COMPATIBLE

PATH:$PROJECT/../codes/MS

MSLABcustominstallation

% STARTMS (PATH: $PROJECT/startms.m) – MATLAB SCRIPT

% MINIMUM setup configuration for MS on UNIX machines

% It works also on WINBOXES (Note: MS was designed on WIN32 machines)

% This script defines two global variables PROJECTPATH (string) and LAMMPS (structure)

% A new user must update PROJECTPATH and possibly some fields in LAMMPS

% PROJECTPATH: defines the main directory for all LAMMPS projects

% When the environment variable $PROJECT exist, its value is assigned to PROJECTPATH (default behavior)

% If not the script definition is used.

% LAMMPS: object used to generate all required BASH scripts to submit a job instance

% (with MPIRUN or not, with SUN GRID ENGINE or not)

% In future versions, this variable will be replaced by a single XML file.

% Customizable fields in LAMMPS include:

% LAMMPS.bin: bin/ directory in PROJECTPATH (all required binaries are assumed to be located there)

% NB: Tools are expected to be located in bin/tools (see MSI2LMP)

% Makefiles are located in PROJECTPATH/make

% LAMMPS.lammps: filename of LAMMPS executable (several versions of LAMMPS can be used according to

MPI, compilation options...)

% LAMMPS.maxnumproc: max number of processors, which can be invoked (theoretically 1000, 16 could be an

acceptable value on MIGALE)

% LAMMPS.email: contact e-mail (use to send e-mails during main job events)

% The local variable localMS define the relative path from the location of startms, where MS is installed.

% By default, MS is outside PROJECT (safe behavior). Update its content to your need.

FILE:$PROJECT/startms.m

MODMOL25‐27Feb 2008,Jouy‐en‐Josas

olivier.vitrac@agroparistech.fr

Thisdocumentisbasedonourowncontribution.

Theresultisfreelydistributablewithoutguaranteeorwarranteeofanykind.

# PIZZA and MSLAB starts within $PROJECT

# example of line to be added/updated in ~/.bashrc

export PROJECT="~/project"

PIZZA.pycustominstallation

#!/usr/local/bin/python –I

# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html

...

# modules needed by pizza.py

import sys, commands, os, string, exceptions, glob, refrom time import clock

# Customization by O. Vitrac

boxname = os.name

if boxname.find("nt") >=0:

PIZZAROOT = os.path.normpath("C:\Data\Olivier\INRA\Codes\mslab\pizza")

print "NT system"

else:

PIZZAROOT = os.path.normpath(os.path.join(os.environ.get('PROJECT'),'pizza'))

print "assume a LINUX machine"

os.chdir(PIZZAROOT)

print "current path: %s (default directory for data)" % os.getcwd()

print "available functions in src:\n\n %s\n" % os.listdir(os.path.normpath(os.path.join(PIZZAROOT,'src')))

...

# ALL SCRIPTS ARE NOW LAUNCHED FROM PIZZAROOT: $PROJECT/pizza

# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html

# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories...

...

import osPIZZA_TOOLS = [os.path.normpath(os.path.join(os.getcwd(),'src'))]

PIZZA_SCRIPTS = [os.path.join(os.getcwd(),'scripts'),os.path.join(os.getcwd(),'examples')]

PIZZA_EXCLUDE = ["pizza", "DEFAULTS", "vizinfo"]

FILE:$PROJECT/pizza/src/pizza.py

FILE:$PROJECT/pizza/src/DEFAULTS.py

CUSTOMPIZZATEST

# simple test of chain tool

# creates tmp.data.chain file (see test_chain.py)

c = chain(500,0.7,1,1,2)

c.seed = 54321

c.build(25,10)

c.mtype = 2

c.btype = 2

c.blen = 1.5

c.dmin = 1.2

c.id = "end1"

c.build(10,25)

c.write("tmp.data.chain")

print "all done ... type CTRL-D to exit Pizza.py"

PIZZA Functions http://www.cs.sandia.gov/~sjplimp/pizza.html

animate.py Animateaseriesofimagefiles

cdata.py Read,write,manipulateChemCell datafiles

chain.py Createbead‐springchainsforLAMMPSinput

cfg.py ConvertLAMMPSsnapshotstoCFGformat

clog.py ReadChemCell logfilesandextractspeciesdata

data.py Read,write,manipulateLAMMPSdatafiles

dump.py Read,write,manipulate dumpfilesandparticle attributes

ensight.py ConvertLAMMPSsnapshotstoEnsight format

gl.py 3dinteractivevisualizationviaOpenGL

gnu.py Create plotsviaGnuPlot plotting program

histo.py Particledensityhistogramfromadump

image.py Viewandmanipulateimages

log.py ReadLAMMPSlogfilesandextractthermodynamicdata

matlab.py CreateplotsviaMatLab numericalanalysisprogram

mdump.py Read,write,manipulatemeshdumpfiles

pair.py ComputeLAMMPSpairwiseenergies

patch.py CreatepatchyLennard‐JonesparticlesforLAMMPSinput

pdbfile.py Read,writePDBfilesincombowithLAMMPSsnapshots

plotview.py Plotmultiplevectorsfromadataset

rasmol.py 3dvisualizationviaRasMol program

raster.py 3dvisualization viaRaster3d program

svg.py 3dvisualizationviaSVG files

vcr.py VCR‐styleGUIfor3dinteractiveOpenGLvisualization

vec.py Createnumericvectorsfromcolumnsinfileorlistofvecs

vtk.py ConvertLAMMPSsnapshotstoVTKformat

xyz.py Convert LAMMPSsnapshots toXYZformat43

PIZZAwith GUI

#ADDtheexportlinetoyour bash ortypeit:

$exportPYTHONPATH="/usr/local/src/public/PyOpenGL‐

3.0.0a6/:/usr/local/src/public/modules‐python/Imaging‐

1.1.6/PIL/:/usr/local/public/python‐2.4.3/lib/python2.4/site‐

packages/Numeric/:/usr/local/genome/mgcat1.24‐linux32‐

py23/:/usr/local/src/public/ctypes‐1.0.2/build/lib.linux‐x86_64‐

2.3/:/usr/local/public/python‐2.4.3/lib/python2.4/site‐packages/setuptools‐0.6c7‐

py2.4.egg/:/usr/local/src/public/Togl‐1.7/"

$\pizza#\isusedtooverride thecurrent alias

ssh –Yusername@topaze.jouy.inra.fr

Check:echo $DISPLAY 44

MODMOL25‐27Feb 2008,Jouy‐en‐Josas

olivier.vitrac@agroparistech.fr

Thisdocumentgathersseveralfreelyavailablesources.

Theresultisfreelydistributablewithoutguaranteeorwarranteeofanykind.

BEAD‐SPRINGPOLYMERMELT

FENE:FiniteExtendibleNonlinearElasticModel(here:2880beads,2715bonds)

$PROJECT/bin/tools/chain <$PROJECT/examples/example.def.chain

>$PROJECT/chain/data.chain

Polymer chain definition

0.8442 rhostar

592984 random # seed (8 digits or less)

2 # of sets of chains (blank line + 6 values for each set)

0 molecule tag rule: 0 = by mol, 1 = from 1 end, 2 = from 2

ends

160 number of chains

16 monomers/chain

1 type of monomers (for output into LAMMPS file)

1 type of bonds (for output into LAMMPS file)

0.97 distance between monomers (in reduced units)

1.02 no distance less than this from site i-1 to i+1 (reduced

unit)

5 number of chains

64 monomers/chain

2 type of monomers (for output into LAMMPS file)

2 type of bonds (for output into LAMMPS file)

1.05 distance between monomers (in reduced units)

1.12 no distance less than this from site i-1 to i+1 (reduced

unit) FILE:$PROJECT/examples/example.def.chain

BEAD‐SPRINGPOLYMERMELT

FENE:FiniteExtendibleNonlinearElasticModel(here:2880beads,2715bonds)

# PIZZA-PYTHON SCRIPT using the method CHAIN

# Such script is equivalent to

# $PROJECT/bin/tools/chain <$PROJECT/examples/example.def.chain

# >$PROJECT/chain/data.chain

N = 2880 # total number of monomers

rhostar = 0.8442 # density

#c = chain(N,rhostar) #setup box with N monomers at reduced density rho

c = chain(N,rhostar,1,1,1) #x,y,z = aspect ratio of box (def = 1,1,1)

c.seed = 592984 #set random # seed (def = 12345)

c.mtype = 1 #set type of monomers (def = 1)

c.btype = 1 #set type of bonds (def = 1)

c.blen = 0.97 #set length of bonds (def = 0.97)

c.dmin = 1.02 #set min dist from i-1 to i+1 site (def = 1.02)

c.build(160,16) #create 160 chains, each of length 16

c.mtype = 2 #set type of monomers (def = 1)

c.btype = 2 #set type of bonds (def = 1)

c.blen = 1.05 #set length of bonds (def = 0.97)

c.dmin = 1.12 #set min dist from i-1 to i+1 site (def = 1.02)

c.build(5,64) #create 5 chains, each of length 64

c.write("data.chain") #write out all built chains to LAMMPS data file

FILE:$PROJECT/pizza/examples/example_chain_data.py

pizza

BEAD‐SPRING

POLYMERMELT

# SCRIPT derived from FENE beadspring benchmark

units lj

atom_style bond

special_bonds 0.0 1.0 1.0

read_data data.chain

neighbor 0.4 bin

neigh_modify every 1 delay 1

bond_style fene

bond_coeff 1 30.0 1.5 1.0 1.0

bond_coeff 2 30.0 1.5 1.0 1.0

pair_style lj/cut 1.20

pair_modify shift yes

pair_coeff 1 1 1.0 1.0 1.12

pair_coeff 2 2 1.5 1.1 1.20

fix 1 all nve

fix 2 all langevin 1.0 1.0 10.0 904297

thermo 100

timestep 0.012

run 10000

160+5‐merchainsandFENEbonds:

2,880monomersfor104timesteps

reduceddensity0.8442(liquid)

forcecutoffof2^(1/6)sigma

neighborskin=0.4sigma

neighbors/atom=5(withinforce

cutoff)

NVEtimeintegration

FENE standsforthefinitely

extensiblenonlinearelastic

modelofalong‐chained

polymer.Itsimplifiesthechain

ofmonomersbyconnectinga

sequenceofbeadswith

nonlinearsprings.Thespring

forcelawisgovernedby

inverseLangevin functionor

approximatedbytheWarner's

relationship:

# DEMO: bidisperse (advanced ex.)

# 26/02/08

echo $PROJECT # current queue

lslam examples # ls available templates

# PROJECT 1) BOX CREATION AND MINIMIZATION

#==========================================

lamjob examples/in.bidisperse.relax script 1test.birelax []

def.chain.bidisperse in.bidisperse.nvt # copy templates, generate scripts

cdlam test.birelax # cd into the new project

$PROJECT/bin/tools/chain <def.chain.bidisperse >data.chain.bidisperse

# generate chains on a lattice

nano in.bidisperse.relax # edit the relaxation script (no change required)

./run.sh # launch/submit the job on a single proc

u# check your job

# STEP 2) NVT DYNAMICS

#=====================

echo $QUEUE # current queue

export QUEUE="stage.q“ # change queue (empty assign the default “long.q”)

lamjob test.birelax/in.bidisperse.nvt run 4test.binvt []

bidisperse.relax.restart.10000 # generate/submit the dynamics on 4 procs

u# check your job 49

FILE:$PROJECT/examples/bidisperse.demo

ALLATOMSIMULATION

EXAMPLE1:CVFF(nowarnings),shrink boundary conditions

units real

atom_style full

boundary s s s

pair_style lj/cut 10.0

bond_style harmonic

angle_style harmonic

dihedral_style harmonic

improper_style none

read_data decane.lammps05

neighbor 2.0 bin

neigh_modify delay 5

timestep 2.0

thermo_style multi

thermo 50

msi2lmp $PROJECT/examples/decane I CVFF

lamjob examples/in.decane script 1 decane [] decane.lammps05

decane

fix 1 all nvt

298.0 298.0 100.0

dump 1 all atom

100 dump.decane

minimize 1.0e-4 100

1000

run 10000

FILE:$PROJECT/examples/in.decane 50

ALLATOMSIMULATION

EXAMPLE2:CVFF(warnings),shrink boundary conditions

msi2lmp $PROJECT/examples/Epicatechin I cvff

lamjob examples/in.Epicatechin script 1 Epicatechin []

Epicatechin.lammps05

Epicatechin

units real

atom_style full

boundary s s s

pair_style lj/cut 10.0

bond_style harmonic

angle_style harmonic

dihedral_style harmonic

improper_style cvff

read_data

Epicatechin.lammps05

neighbor 2.0 bin

neigh_modify delay 5

timestep 2.0

thermo_style multi

thermo 50

fix 1 all nvt

298.0 298.0 100.0

dump 1 all atom

100 dump.decane

minimize 1.0e-4 100

1000

run 10000

FILE:$PROJECT/examples/in.Epicatechin

ALLATOMSIMULATION

EXAMPLE3:CFF(warnings),periodic boundary conditions,NPT

msi2lmp $PROJECT/examples/BHT/ethanol_BHTx1 II cff91

lamjob examples/BHT/in.ethanol_BHTx1 script 1 BHT []

ethanol_BHTx1.lammps05

BHTin200

molecules

ofethanol

units real

atom_style full

boundary p p p

pair_style lj/cut/coul/cut 10.0

8.0

bond_style class2

angle_style class2

dihedral_style class2

improper_style class2

read_data

ethanol_BHTx1.lammps05

neighbor 2.0 bin

neigh_modify delay 5

timestep 1.0

thermo_style multi

thermo 50

fix 1 all npt

298.0 298.0 100.0 xyz 1.0

1.0 1.0

dump 1 all atom

1000 dump.ethanol_BHTx1

run 10000

FILE:$PROJECT/examples/BHT/in.ethanol_BHTx1

MODMOL25‐27Feb 2008,Jouy‐en‐Josas

olivier.vitrac@agroparistech.fr

Thisdocumentgathersseveralfreelyavailablesources.

Theresultisfreelydistributablewithoutguaranteeorwarranteeofanykind.

LEARNINGPYTHON

LEARNINGMATLAB

http://www.mathworks.com/access/

helpdesk/help/techdoc/index.html?/

access/helpdesk/help/techdoc/learn_

matlab/bqr_2pl.html 57

VISUALIZATIONOFDUMPFILES

http://www.ks.uiuc.edu/Development/Download/do

wnload.cgi?PackageName=VMD

Version1.8.6(2007‐04‐07)

WIN2LINUXSolutions

#Cygwin withSSHD:requireszlib,tcpwrappers,openssh

#Install

mkpasswd ‐l>/etc/passwd

mkgroup ‐l>/etc/group

exit

#Relogin

which sshd

ssh‐host‐config‐y

cygrunsrv ‐Ssshd

sc descriptionsshd

#create publickey

ssh‐keygen ‐tdsa

#send key

cat.ssh/*.pub|ssh ovitrac@topaze.jouy.inra.frtee‐a.ssh/authorized_keys

#autologin

ssh ovitrac@topaze.jouy.inra.fr

http://www.chiark.greenend.org.uk/~sgtat

ham/putty/download.html

(free)

http://cygwin.com/

(free)

WIN2LINUXSolutions

http://sourceforge.net/projects/xming

(free)

http://winscp.net/eng/docs/lang:fr

(free)

WIN2LINUXSolutions

http://www.sftpdrive.com/

SHAREWARE

http://www.vmware.com/products/server/

(VMWARESERVER:currently Free) 63

MODMOL25‐27Feb 2008,Jouy‐en‐Josas

olivier.vitrac@agroparistech.fr

Thisdocumentgathersseveralfreelyavailablesources.

Theresultisfreelydistributablewithoutguaranteeorwarranteeofanykind.

$PROJECT\make\lammps‐

31Jan08\src\MAKE\Makefile.g++_lam_all_100208

•#g++=RedHat Linuxbox,g++,LAM,FFTW

•#INRA\OlivierVitrac13/02/08(forLAMMPS10/02/08)

•#

•#Compilationis ok

•#>>TESTEXAMPLE:

•#>>cd$PROJECT/../testlam;./lmp_g++_lam<in.lj

•#

•#>>BUGREPORT

•#TheMPIRUNhangs.

•#cd$PROJECT/../testlam;lamboot;mpirun ‐np 1

lmp_g++_lam <in.lj

•

•SHELL=/bin/sh

•#.IGNORE:

•

•#System‐specific settings

•CC=g++

•CCFLAGS=‐g‐O‐I/usr/local/public/lam/include \

•‐I/usr/include ‐DFFT_FFTW‐DLAMMPS_GZIP‐

DMPICH_IGNORE_CXX_SEEK

•DEPFLAGS=‐M

•LINK=g++

•LINKFLAGS=‐g‐O‐L/usr/local/public/lam/lib\

•‐L/usr/lib64

•USRLIB=‐lfftw ‐llammpio ‐llammpi++‐llamf77mpi‐lmpi ‐

llam

•SYSLIB=‐lpthread ‐ldl

•ARCHIVE=ar

•ARFLAGS=‐rc

•SIZE=size

•

•#Linktarget

•$(EXE):$(OBJ)

•$(LINK)$(LINKFLAGS)$(OBJ)$(USRLIB)$(SYSLIB)‐o$(EXE)

•$(SIZE)$(EXE)

•

•#Librarytarget

•lib:$(OBJ)

•$(ARCHIVE)$(ARFLAGS)$(EXE)$(OBJ)

•

•#Compilationrules

•%.o:%.cpp

•$(CC)$(CCFLAGS)‐c$<

•%.d:%.cpp

•$(CC)$(CCFLAGS)$(DEPFLAGS)$<>$@

•

•#Individual dependencies

•DEPENDS=$(OBJ:.o=.d)

•include $(DEPENDS)

1 LAMMPS Short Manual

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