├── README.md ├── index.html └── lammps_tutorial ├── FENE.png ├── LJ.png ├── LJattract.png ├── LangevinEqn.gif ├── cosine.png ├── dump.spheres ├── eta.gif ├── gamma.gif ├── generate_ic ├── generate_DNA.h ├── generate_functions.cc └── generate_linear.cc ├── log.lammps ├── plots.gplot ├── spheres.restart.10000 ├── spheres.restart.5000 ├── tutorial2 ├── diffusing_particle.lam └── initial_configuration.txt ├── tutorial3 ├── initial_configuration.txt ├── many_particles.lam └── many_particles.lam~ ├── tutorial4 ├── initial_configuration.txt └── polymer.lam ├── tutorial5 ├── initial_configuration.txt ├── polymer+switchingbridges.lam └── polymer_plus_bridges.lam ├── tutorial6 ├── initial_configuration.txt ├── old_initial_configuration.txt ├── setup │ ├── README │ ├── a.out │ ├── add_links │ ├── dump_1stequilib.DNA │ ├── dump_2ndequilib.DNA │ ├── equilibrated_loops.data │ ├── in.twistDNA_1stequilib │ ├── in.twistDNA_2ndequilib │ ├── initial_configuration.txt │ ├── lammps.input │ ├── lammps_restart2data_with_ellipsoids.sh │ ├── linking_1stequilib.dat │ ├── measure_linking │ ├── restart.1stequilib │ ├── restart.2ndequilib │ ├── thermo.first_equilib │ └── thermo_2ndequilib.dat └── supercoiled.lam └── vmdrc /README.md: -------------------------------------------------------------------------------- 1 | # simple_lammps_tutorial 2 | A simple tutorial for simulating polymers in LAMMPS. 3 | -------------------------------------------------------------------------------- /index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
9 | 10 |

A very basic LAMMPS tutorial

 11 | 12 |

13 | 14 | This is a very simple and quick tutorial on how to use LAMMPS to simulate a polymer using Langevin dynamics. I've tried to add links to the LAMMPS manual and other sources where appropriate. The input scripts include further comments detailing what each command does. 15 | 16 |

17 | 18 |

1. Compiling LAMMPS

 19 | 20 | The LAMMPS source code can be downloaded as a tarball from the LAMMPS website: lammps.sandia.gov/download.html. 21 | 22 |

23 | 24 | To compile with the basic packages, download and unpack, switch to the src/ directory and type: 25 | 26 | 
 make serial
or 
 make mpi
to compile serial or mpi versions. All the packages required to do the simulations in 2-5 below should be enabled by default (if you download via git checkout you might need to install them). For section 6 LAMMPS must be compiled with the ASPHERE packages and some additional custom interaction styles. 27 | 28 |

29 | 30 | 37 | 38 |

2. First simulation - a diffusing particle

 39 | 40 | The way we will use LAMMPS requires two input files: a script which tells LAMMPS what to do, and an initial configuration file which gives the initial coordinates of each atom in the system, as well as other information. 41 | 42 |

43 | 44 | For the first example we will simulate a single atom diffusing in an implicit solvent. The input script and initial conditions files are diffusing_particle.lam and initial_configuration.txt. 45 | 46 | To run LAMMPS using these files, download them to a new directory where there is a copy of the LAMMPS executable and type 
 ./lmp_serial < diffusing_particle.lam
Some messages will be printed to the screen, and some output files created. Look at the comments in the in.diffusing_particle file for details of each command. The configuration file cannot contain any comments, but the details of how to lay out this file are here in the LAMMPS manual. The output files include a "dump file" which contains the positions of the atom at regular time steps, and a "thermo file" which contains thermodynamic information at regular time steps. The dump file can be loaded into e.g. vmd to visualize the simulation trajectory (see below). 47 | 48 |

49 | 50 | Here were are using LAMMPS to run a Langevin Dynamics simulation (sometimes called Brownian Dynamics), where the position of atoms are described by a Langevin equation 51 |
52 | langevin equation 53 |
54 | where atoms experience random forces (\eta) and viscous drag (\gamma) from an implied solvent. In LAMMPS we use the NVE and langevin fixes, which results in an NVT system (canonical ensemble); LAMMPS uses a velocity-Verlet update rule. In this simulation the particle is diffusing in a "periodic box", i.e. if the particle moves out of one the edge of the box, it appears on the other side of the box. LAMMPS keeps track of movement through the periodic boundaries. 55 | 56 |

57 | 58 | To view the dump file in VMD, choose "New Molecule" from the file menu, click browse to find the file, and select "LAMMPS Trajectory" from the drop down list before hitting "Load". Depending on the version of VMD, it may or may not "unwrap" the periodic boundaries if the particle moves through them. To wrap all atoms back into the periodic box, paste the following command on to the VMD command line: 
 pbc wrap -all
59 | 60 | To set some of the default options in VMD so that they are more appropriate for these kinds of simulations, download this vmdrc file and move it in your home directory renamed with a '.' at the start (~/.vmdrc). VMD should read it automatically when it starts. 61 | 62 |

63 | 64 |

3. Many diffusing particles

 65 | 66 | Similar to the above, here we simulate particles diffusing in an implicit solvent. Now though, we introduce a Weeks-Chandler-Anderson (WCA; also called a shifted, truncated Lennard Jones, LJ) interaction potential between the particles, so that they cannot overlap. 67 |
68 | LJ potential 69 |             70 |

71 | 72 | In LAMMPS the WCA potential is obtained by using the LJ potential and selecting an appropriate cut-off (i.e. the cut-off is chosen at the minimum of the potential so there is no attractive part). 73 | 74 |

75 | 76 | An initial conditions file is generated by choosing random x,y,z coordinates for each of the atoms. This means that there is a chance that initially some of the atoms might overlap. Since the LJ potential has a very strong short range repulsion, these overlapping atoms would experience very large forces in the first few steps of the simulation - LAMMPS would crash with an error. To prevent this we first run a short "equilibration simulation" using a different "softer" interaction potential: the atoms will be slowly pushed apart. Then we can switch to the LJ interactions. 77 | 78 |

79 | 80 | Download the LAMMPS script many_particles.lam and configuration file initial_configuration.txt to a new directory with a copy of the LAMMPS executable and run as follows 
 ./lmp_serial < many_particles.lam
81 | 82 | In addition to a dump file and a thermo file, this script also uses a LAMMPS compute command to calculate the mean squared displacement (MSD) of all the atoms as a function of time. 83 | 84 |

85 | 86 |

4. Join the atoms together into a polymer

 87 | 88 | In this simulation the atoms are joined together in a chain to form a simple "bead-and-spring" polymer. The configuration file initial_configuration.txt now also contains a list of "bonds" and "angles" telling LAMMPS how the atoms are connected. The initial positions of the atoms are along the path of a random walk with step size 1, so that they are in a chain. 89 | 90 |

91 | 92 | We connect the atoms using finite-extensible non-linear (FENE) springs, and add and angle interaction between triplets of atoms so as to give the polymer some bending rigidity. As before we use an WCA interaction between the atoms so that they cannot overlap. 93 |
94 | FENE potential 95 | Bending potential 96 |

97 | 98 | Again, with these initial conditions is is possible (highly likely) that some atoms will overlap. To avoid the atoms experiencing large forces (which will lead to bonds being highly stretched and LAMMPS crashing) we run an equilibrium simulation using a "soft" pair interaction potential, and a "harmonic" bond interaction. 99 | 100 |

101 | 102 | To run, download the script polymer.lam and initial_configuration.txt to a new directory containing the LAMMPS executable, and us the command 
 ./lmp_serial < polymer.lam
103 | 104 | This time, as well as the dump and thermo files, a LAMMPS compute is used to calculate the radius of gyration of the polymer (a measure of its size in 3D space). 105 | 106 |

107 | 108 |

5. Polymer + bridges

 109 | 110 | In this simulation we have both a chain of beads forming a polymer, and several un-linked beads. The un-linked beads have both a short range repulsive and a longer range attractive interaction with the polymer beads, for which we use an LJ interaction with a larger cut-off than before. 111 | 112 |
113 | FENE potential 114 |

115 | 116 | We add repulsive interactions between polymer beads, and between un-linked beads. Together this means that the un-linked beads can stick to the polymer; since they can stick to more than one polymer bead at a time, they can form bridges between polymer beads. 117 | 118 |

119 | 120 | As before we run a short equilibration simulation at the start, to push atoms apart slowly, before switching to LJ and FENE potentials. We then also add a further run where the attractive interactions are switched off, before switching them on. Again a compute is used to calculate the gyration radius of the polymer. By plotting this you will see the effect of the attractive interactions between the polymer and non-polymer beads. 121 | 122 |

123 | 124 | To run, download the script polymer_plus_bridges.lam and initial_configuration.txt to a new directory containing the LAMMPS executable, and us the command 
 ./lmp_serial < polymer+bridges.lam
125 | 126 |

127 | 128 |

6. Supercoiled Polymer

 129 | 130 | Finally we will use the polymer model with torsional rigidity developed in the paper J. Chem. Phys. 140, 135103 (2014) (arxiv) to simulate a supercoiled loop. For this, two custom angle interaction potential are required (available here with instructions on how to recompile LAMMPS), and we will use the ellipse atoms style. With this style atoms have an orientation as well as a position. LAMMPS must be compiled with the "ASPHERE" package installed: run the command 
make yes-asphere
before compiling. 131 | 132 |

133 | 134 | The initial_configuration.txt file is set up with an un-writhed loop which has had three excess units of twist added to it. This has already been equilibrated, so there is no need to run with soft potentials. The LAMMPS script supercoiled.lam runs a simulation where the loop will relax such that the excess twist will be converted to writhe. The dump file which is generated will also contain a quaternion for each atom describing its orientation. 135 | 136 |

137 | 138 |

Some notes on real simulations

 139 | 140 |
    141 |
  1. Equilibration: For these examples with only a small number of atoms, we have included the equilibration simulation as part of the same script as the main simulation. Since this uses unrealistic interaction potentials, and for larger systems will take longer to run, for a real simulation a separate equilibration script is usually used to generate an equilibrated conformation. The restart file from this can then be used to initialize the main simulation (and we are only interested in those trajectories). We can then re-use the same equilibrated conformation for multiple simulations.
    2. 142 |
  2. Random Numbers: Using the langevin fix adds random thermal motion to the simulation; the sequence of pseudo-random numbers used depends on the seed entered. We often want to run many repeat simulations in order to calculate ensemble average properties - for each repeat we would want to use a different seed and a different initial condition. It is also straightforward to set up loops in the LAMMPS script to run multiple repeat simulations one after the other, as detailed here.
    3. 143 |
  3. Parallelization: For simulating larger systems we can run LAMMPS on multiple processors using mpi; above we have run LAMMPS in serial mode. To run in parallel all we have to do is invoke LAMMPS via the mpirun command, specifying the number of processors to use as detailed here.
    4. 144 |
145 | 146 |

147 | 148 | 149 | 150 | -------------------------------------------------------------------------------- /lammps_tutorial/FENE.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/FENE.png -------------------------------------------------------------------------------- /lammps_tutorial/LJ.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/LJ.png -------------------------------------------------------------------------------- /lammps_tutorial/LJattract.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/LJattract.png -------------------------------------------------------------------------------- /lammps_tutorial/LangevinEqn.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/LangevinEqn.gif -------------------------------------------------------------------------------- /lammps_tutorial/cosine.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/cosine.png -------------------------------------------------------------------------------- /lammps_tutorial/dump.spheres: -------------------------------------------------------------------------------- 1 | ITEM: TIMESTEP 2 | 0 3 | ITEM: NUMBER OF ATOMS 4 | 1 5 | ITEM: BOX BOUNDS pp pp pp 6 | -50 50 7 | -50 50 8 | -50 50 9 | ITEM: ATOMS id type xs ys zs 10 | 1 1 0.5 0.5 0.5 11 | ITEM: TIMESTEP 12 | 1000 13 | ITEM: NUMBER OF ATOMS 14 | 1 15 | ITEM: BOX BOUNDS pp pp pp 16 | -50 50 17 | -50 50 18 | -50 50 19 | ITEM: ATOMS id type xs ys zs 20 | 1 1 0.500681 0.49587 0.596681 21 | ITEM: TIMESTEP 22 | 2000 23 | ITEM: NUMBER OF ATOMS 24 | 1 25 | ITEM: BOX BOUNDS pp pp pp 26 | -50 50 27 | -50 50 28 | -50 50 29 | ITEM: ATOMS id type xs ys zs 30 | 1 1 0.558203 0.553961 0.636815 31 | ITEM: TIMESTEP 32 | 3000 33 | ITEM: NUMBER OF ATOMS 34 | 1 35 | ITEM: BOX BOUNDS pp pp pp 36 | -50 50 37 | -50 50 38 | -50 50 39 | ITEM: ATOMS id type xs ys zs 40 | 1 1 0.557796 0.541153 0.610399 41 | ITEM: TIMESTEP 42 | 4000 43 | ITEM: NUMBER OF ATOMS 44 | 1 45 | ITEM: BOX BOUNDS pp pp pp 46 | -50 50 47 | -50 50 48 | -50 50 49 | ITEM: ATOMS id type xs ys zs 50 | 1 1 0.572172 0.55842 0.583949 51 | ITEM: TIMESTEP 52 | 5000 53 | ITEM: NUMBER OF ATOMS 54 | 1 55 | ITEM: BOX BOUNDS pp pp pp 56 | -50 50 57 | -50 50 58 | -50 50 59 | ITEM: ATOMS id type xs ys zs 60 | 1 1 0.662661 0.540306 0.62843 61 | ITEM: TIMESTEP 62 | 6000 63 | ITEM: NUMBER OF ATOMS 64 | 1 65 | ITEM: BOX BOUNDS pp pp pp 66 | -50 50 67 | -50 50 68 | -50 50 69 | ITEM: ATOMS id type xs ys zs 70 | 1 1 0.682236 0.47217 0.66244 71 | ITEM: TIMESTEP 72 | 7000 73 | ITEM: NUMBER OF ATOMS 74 | 1 75 | ITEM: BOX BOUNDS pp pp pp 76 | -50 50 77 | -50 50 78 | -50 50 79 | ITEM: ATOMS id type xs ys zs 80 | 1 1 0.676258 0.462116 0.588718 81 | ITEM: TIMESTEP 82 | 8000 83 | ITEM: NUMBER OF ATOMS 84 | 1 85 | ITEM: BOX BOUNDS pp pp pp 86 | -50 50 87 | -50 50 88 | -50 50 89 | ITEM: ATOMS id type xs ys zs 90 | 1 1 0.644823 0.5134 0.558574 91 | ITEM: TIMESTEP 92 | 9000 93 | ITEM: NUMBER OF ATOMS 94 | 1 95 | ITEM: BOX BOUNDS pp pp pp 96 | -50 50 97 | -50 50 98 | -50 50 99 | ITEM: ATOMS id type xs ys zs 100 | 1 1 0.628129 0.561316 0.575277 101 | ITEM: TIMESTEP 102 | 10000 103 | ITEM: NUMBER OF ATOMS 104 | 1 105 | ITEM: BOX BOUNDS pp pp pp 106 | -50 50 107 | -50 50 108 | -50 50 109 | ITEM: ATOMS id type xs ys zs 110 | 1 1 0.601814 0.561056 0.534079 111 | -------------------------------------------------------------------------------- /lammps_tutorial/eta.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/eta.gif -------------------------------------------------------------------------------- /lammps_tutorial/gamma.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/gamma.gif -------------------------------------------------------------------------------- /lammps_tutorial/generate_ic/generate_DNA.h: -------------------------------------------------------------------------------- 1 | 2 | using namespace std; 3 | 4 | struct myenums { 5 | int BEND, TORS, TORSEND, 6 | DNADNA, 7 | DNA, DPAT, NCORE, NPAT1, NPAT2, PCORE, PPAT; 8 | myenums() { 9 | BEND=1; TORS=2; TORSEND=3; 10 | DNADNA=1; 11 | DNA=1; DPAT=2; NCORE=3; NPAT1=4; NPAT2=5; PCORE=6; PPAT=7; 12 | } 13 | } TYPE; 14 | 15 | struct bond { 16 | bond(int aa, int bb, int t) : a(aa), b(bb), type(t) {}; 17 | int a,b, 18 | type; 19 | }; 20 | 21 | struct angle { 22 | angle(int aa, int bb, int cc, int t) : a(aa), b(bb), c(cc), type(t) {}; 23 | int a,b,c, 24 | type; 25 | }; 26 | 27 | struct evec { 28 | double ei,ej,ek; 29 | evec cross(evec a) { 30 | evec c; 31 | c.ei=ej*a.ek - ek*a.ej; 32 | c.ej=ek*a.ei - ei*a.ek; 33 | c.ek=ei*a.ej - ej*a.ei; 34 | return c; 35 | } 36 | double length() { 37 | return sqrt(ei*ei + ej*ej + ek*ek); 38 | } 39 | void make_unit() { // makes it a unit vector 40 | double l; 41 | l=length(); 42 | ei/=l; 43 | ej/=l; 44 | ek/=l; 45 | } 46 | }; 47 | 48 | struct quaternion { 49 | double q0,q1,q2,q3; 50 | double norm(); 51 | void make_quat(evec, evec, evec); 52 | evec xaxis(); 53 | private : 54 | double sign(double); 55 | }; 56 | 57 | struct atom { 58 | atom(double a,double b, double c) : x(a), y(b), z(c) {}; 59 | atom() {} 60 | double x,y,z,density; 61 | double q[4]; 62 | int id, 63 | type, 64 | mol, 65 | ellipse_flag; 66 | void quat(quaternion quat) { 67 | q[0]=quat.q0; 68 | q[1]=quat.q1; 69 | q[2]=quat.q2; 70 | q[3]=quat.q3; 71 | } 72 | }; 73 | 74 | void output_tors(ostream&,vector&); 75 | void output_notors(ostream&,vector&); 76 | 77 | void do_dna_randlin(vector&,vector&,vector&); 78 | 79 | double quaternion::norm() { 80 | 81 | return sqrt(q0*q0 + q1*q1 + q2*q2 + q3*q3); 82 | 83 | } 84 | 85 | double quaternion::sign(double x) {return (x >= 0.0) ? +1.0 : -1.0;} 86 | 87 | void quaternion::make_quat(evec xax, evec yax, evec zax) { 88 | 89 | double r11,r12,r13, 90 | r21,r22,r23, 91 | r31,r32,r33, 92 | r; 93 | 94 | r11=xax.ei; r21=xax.ej; r31=xax.ek; 95 | r12=yax.ei; r22=yax.ej; r32=yax.ek; 96 | r13=zax.ei; r23=zax.ej; r33=zax.ek; 97 | 98 | q0=( r11 + r22 + r33 + 1.0f) / 4.0; 99 | q1=( r11 - r22 - r33 + 1.0f) / 4.0; 100 | q2=(-r11 + r22 - r33 + 1.0f) / 4.0; 101 | q3=(-r11 - r22 + r33 + 1.0f) / 4.0; 102 | 103 | if(q0 < 0.0) q0 = 0.0; 104 | if(q1 < 0.0) q1 = 0.0; 105 | if(q2 < 0.0) q2 = 0.0; 106 | if(q3 < 0.0) q3 = 0.0; 107 | 108 | q0 = sqrt(q0); 109 | q1 = sqrt(q1); 110 | q2 = sqrt(q2); 111 | q3 = sqrt(q3); 112 | 113 | if(q0 >= q1 && q0 >= q2 && q0 >= q3) { 114 | q0 *= +1.0f; 115 | q1 *= sign(r32 - r23); 116 | q2 *= sign(r13 - r31); 117 | q3 *= sign(r21 - r12); 118 | } else if(q1 >= q0 && q1 >= q2 && q1 >= q3) { 119 | q0 *= sign(r32 - r23); 120 | q1 *= 1.0; 121 | q2 *= sign(r21 + r12); 122 | q3 *= sign(r13 + r31); 123 | } else if(q2 >= q0 && q2 >= q1 && q2 >= q3) { 124 | q0 *= sign(r13 - r31); 125 | q1 *= sign(r21 + r12); 126 | q2 *= 1.0; 127 | q3 *= sign(r32 + r23); 128 | } else if(q3 >= q0 && q3 >= q1 && q3 >= q2) { 129 | q0 *= sign(r21 - r12); 130 | q1 *= sign(r31 + r13); 131 | q2 *= sign(r32 + r23); 132 | q3 *= 1.0; 133 | } else { 134 | cout<<"quaternion error"<& atoms) { 2 | 3 | ouf<& atoms) { 22 | 23 | 24 | ouf< &atoms,vector &bonds,vector &angles, double box[3], double de, double density) { 38 | // Add a DNA bead to the random configuration 39 | 40 | double theta,phi, 41 | dx,dy,dz, 42 | hbox[3],id; 43 | 44 | for (int i=0;i<3;i++) { 45 | hbox[i]=box[i]*0.5; 46 | } 47 | 48 | // position 49 | do { 50 | theta=double(rand())/double(RAND_MAX)*PI; 51 | phi=double(rand())/double(RAND_MAX)*2.0*PI; 52 | dx=last.x+sin(theta)*cos(phi); 53 | dy=last.y+sin(theta)*sin(phi); 54 | dz=last.z+cos(theta); 55 | } while (abs(dx)>hbox[0]||abs(dy)>hbox[1]||abs(dz)>hbox[2]); // reject if outside box 56 | 57 | id=atoms.back().id; 58 | 59 | id++; 60 | atoms.push_back( atom(dx,dy,dz) ); 61 | atoms.back().type=TYPE.DNA; 62 | atoms.back().id=id; 63 | atoms.back().mol=last.mol; 64 | atoms.back().ellipse_flag=1; 65 | atoms.back().density=density; 66 | 67 | // oreintation 68 | atoms.back().q[0]=1; atoms.back().q[1]=0; atoms.back().q[2]=0; atoms.back().q[3]=0; 69 | 70 | // bond 71 | bonds.push_back( bond(last.id,atoms.back().id,TYPE.DNADNA) ); 72 | 73 | // angle 74 | if (lastlast.id==0) { // this is bead number 2 75 | angles.push_back( angle(last.id,atoms.back().id,atoms.back().id,TYPE.TORS) ); // the third id here does nothing 76 | } else { 77 | angles.push_back( angle(lastlast.id,last.id,atoms.back().id,TYPE.BEND) ); 78 | angles.push_back( angle(last.id,atoms.back().id,atoms.back().id,TYPE.TORS) ); // the third id here does nothing 79 | } 80 | 81 | 82 | } 83 | 84 | 85 | 86 | void add_DNA(atom last,atom lastlast,vector &atoms,vector &bonds,vector &angles, double density, double x,double y,double z) { 87 | // Add a DNA bead to the loop configuration 88 | 89 | atoms.push_back( atom(x,y,z) ); 90 | atoms.back().type=TYPE.DNA; 91 | atoms.back().id=last.id+1; 92 | atoms.back().mol=last.mol; 93 | atoms.back().ellipse_flag=1; 94 | atoms.back().density=density; 95 | 96 | // oreintation 97 | atoms.back().q[0]=1; atoms.back().q[1]=0; atoms.back().q[2]=0; atoms.back().q[3]=0; 98 | 99 | // bond 100 | bonds.push_back( bond(last.id,atoms.back().id,TYPE.DNADNA) ); 101 | 102 | // angle 103 | if (lastlast.id==0) { // this is bead number 2 104 | angles.push_back( angle(last.id,atoms.back().id,atoms.back().id,TYPE.TORS) ); // the third id here does nothing 105 | } else { 106 | angles.push_back( angle(lastlast.id,last.id,atoms.back().id,TYPE.BEND) ); 107 | angles.push_back( angle(last.id,atoms.back().id,atoms.back().id,TYPE.TORS) ); // the third id here does nothing 108 | } 109 | 110 | } 111 | -------------------------------------------------------------------------------- /lammps_tutorial/generate_ic/generate_linear.cc: -------------------------------------------------------------------------------- 1 | // Generate a random linear DNA 2 | // with spherical proteins or nucleosome cores 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | #define PI 3.14159265358979 13 | 14 | #include "generate_DNA.h" 15 | #include "generate_functions.cc" 16 | 17 | //#include "nucleosome.cc" 18 | 19 | using namespace std; 20 | 21 | int main() { 22 | 23 | int N, // DNA length 24 | S, // size of side of grid if loop 25 | Nnuc, // number of nucleosomes 26 | Natpernuc, // number of atoms per nucleosome 27 | Nprot, // number of proteins 28 | nuc_flag, // nucleosomes 29 | prot_flag, // proteins 30 | Dpatch_flag, // patches on DNA? 31 | Ppatch_flag, // patches on proteins? 32 | Nppatch, // number of patches on proteins 33 | tors_flag, // flag for if DNA is to have torsional stifness 34 | loop_flag, // flag for DNA arrangement 35 | Nfiles, // number of files to generate 36 | seed; // for randoms 37 | 38 | double lx,ly,lz, // box size 39 | density, // density of DNA beads 40 | dp_sep, // separation of DNA bead and patch 41 | pp_sep, // separation of protein and patch 42 | dp_angle; // DNA patch orientation offset angle 43 | 44 | stringstream fn; // file name 45 | ofstream ouf; 46 | 47 | vector atoms; 48 | vector bonds; 49 | vector angles; 50 | 51 | 52 | // get parameters 53 | lconfig: 54 | cout<<"DNA configuration : Enter 1 for loop, 0 for random linear"<>loop_flag; 56 | if (loop_flag!=1 && loop_flag!=0) {goto lconfig;} 57 | 58 | cout<<"Length of DNA : "<>N; 60 | if (loop_flag==1) { 61 | S=sqrt(N); if (S%2 == 1) S++; N=S*S; 62 | cout<<"Using "<>lx>>ly>>lz; 68 | if (loop_flag==1 && (lx<1.5*S || ly<1.5*S || lz<1.5*S) ) {cout<<"Box too small."<>tors_flag; 73 | if (tors_flag!=0 && tors_flag!=1) {goto ltors;} 74 | 75 | ldpat: 76 | cout<<"Add patches to DNA? Enter 0 for no, 1 for yes : "<>Dpatch_flag; 78 | if (Dpatch_flag!=0 && Dpatch_flag!=1) {goto ldpat;} 79 | if (Dpatch_flag) { 80 | cout<<"Enter orientational offset angle (degrees) for patch compared to DNA bead orientation : "<>dp_angle; 82 | } 83 | 84 | //cout<<"Number of nucleosome cores : "<>Nnuc; 85 | //if (Nnuc>0) {nuc_flag=1;} else {nuc_flag=0;} 86 | nuc_flag=0; 87 | 88 | cout<<"Number of other proteins : "<>Nprot; 89 | if (Nprot>0) { 90 | prot_flag=1; 91 | lppat: 92 | cout<<"Add patches to proteins? Enter 0 for no, 1 for yes : "<>Ppatch_flag; 94 | if (Ppatch_flag!=0 && Ppatch_flag!=1) {goto lppat;} 95 | if (Ppatch_flag==1) { 96 | nppat: 97 | cout<<"Number of patches on proteins? Enter 1 or 2 : "<>Nppatch; 99 | if (Nppatch!=1 && Nppatch!=2) {goto nppat;} 100 | cout<<"Distance to patch (default 0.4)"<>pp_sep; 102 | } 103 | } else {prot_flag=0;} 104 | 105 | cout<<"Number of files to generate : "<>Nfiles; 106 | 107 | cout<<"Enter seed for random numbers : "<>seed; 108 | 109 | 110 | // set up atom types 111 | if (Dpatch_flag==0) {TYPE.DPAT=0; TYPE.NCORE--; TYPE.NPAT1--; TYPE.NPAT2--; TYPE.PCORE--; TYPE.PPAT--;} 112 | if (Nnuc==0) {TYPE.NCORE=0; TYPE.NPAT1=0; TYPE.NPAT2=0; TYPE.PCORE-=3; TYPE.PPAT-=3;} 113 | 114 | // set other parameters 115 | density=(1-0.1*Dpatch_flag)*6.0/PI; 116 | dp_sep=0.4; // set dna-patch separation 117 | //pp_sep=0.4; // set protein-patch separation 118 | srand(seed); 119 | //if (nuc_flag) { Natpernuc=nucleosome().natom(); } 120 | 121 | 122 | // loop round files 123 | for (int filenum=1;filenum<=Nfiles;filenum++) { 124 | 125 | // file name 126 | fn.clear(); 127 | fn.str(""); 128 | if (Nfiles==1) { 129 | fn<<"lammps.input"; 130 | } else { 131 | fn<<"lammps.input_"<0) { 299 | int id=atoms.back().id, 300 | mol=atoms.back().mol; 301 | double x,y,z; 302 | for (int i=0;i().swap(atoms); 398 | bonds.clear(); vector().swap(bonds); 399 | angles.clear(); vector().swap(angles); 400 | 401 | } 402 | 403 | 404 | 405 | } 406 | 407 | 408 | 409 | -------------------------------------------------------------------------------- /lammps_tutorial/log.lammps: -------------------------------------------------------------------------------- 1 | LAMMPS (7 Dec 2015) 2 | ############################################### 3 | # LAMMPS script for a single particle 4 | ############################################### 5 | 6 | ### 7 | # Box and units (use LJ units and periodic boundaries) 8 | ### 9 | 10 | units lj # use lennard-jones (i.e. dimensionless) units 11 | atom_style atomic # simplest point-like atom type 12 | 13 | boundary p p p # all boundaries are periodic 14 | 15 | ### 16 | # Pair interactions require lists of neighbours to be calculated 17 | ### 18 | neighbor 1.9 bin 19 | neigh_modify every 1 delay 1 check yes 20 | 21 | ### 22 | # Generate RESTART file to store state of simulation 23 | ### 24 | restart 5000 spheres.restart 25 | 26 | ### 27 | # READ "initial configuration" data file 28 | ### 29 | read_data initial_configuration.txt 30 | orthogonal box = (-50 -50 -50) to (50 50 50) 31 | 1 by 1 by 1 MPI processor grid 32 | reading atoms ... 33 | 1 atoms 34 | #read_restart DNA.restart 35 | 36 | ### 37 | # Reset timestep 38 | ### 39 | reset_timestep 0 40 | 41 | ### 42 | # Define groups 43 | ### 44 | group all type 1 #(atom type 1 is group 'all') 45 | 1 atoms in group all 46 | 47 | ### 48 | # Dump configurations at regular intervals 49 | ### 50 | dump dum1 all atom 1000 dump.spheres 51 | 52 | ### 53 | # Set up interaction potentials 54 | ### 55 | # we only have one particle, so nothing to interaction with 56 | # but lammps complains if we don't specify a potential 57 | pair_style lj/cut 1.12246152962189 58 | pair_coeff 1 1 1.0 1.0 1.12246152962189 59 | 60 | 61 | ### 62 | # Set up fixes 63 | ### 64 | variable seed equal 54654651 # a seed for the thermostat 65 | 66 | fix 1 all nve # NVE integrator 67 | fix 2 all langevin 1.0 1.0 1.0 ${seed} # langevin thermostat 68 | fix 2 all langevin 1.0 1.0 1.0 54654651 69 | 70 | ##### Output thermodynamic info (temperature, energy, pressure, etc.) ##### 71 | thermo 1000 72 | thermo_style custom step temp epair emol press vol 73 | ############################################################################ 74 | 75 | ### 76 | # set timestep of integrator 77 | ### 78 | timestep 0.01 79 | 80 | 81 | run 10000 82 | Neighbor list info ... 83 | 1 neighbor list requests 84 | update every 1 steps, delay 1 steps, check yes 85 | max neighbors/atom: 2000, page size: 100000 86 | master list distance cutoff = 3.02246 87 | ghost atom cutoff = 3.02246 88 | binsize = 1.51123 -> bins = 67 67 67 89 | Memory usage per processor = 4.28218 Mbytes 90 | Step Temp E_pair E_mol Press Volume 91 | 0 0 0 0 0 1000000 92 | 1000 0 0 0 0 1000000 93 | 2000 0 0 0 0 1000000 94 | 3000 0 0 0 0 1000000 95 | 4000 0 0 0 0 1000000 96 | 5000 0 0 0 0 1000000 97 | 6000 0 0 0 0 1000000 98 | 7000 0 0 0 0 1000000 99 | 8000 0 0 0 0 1000000 100 | 9000 0 0 0 0 1000000 101 | 10000 0 0 0 0 1000000 102 | Loop time of 0.0254099 on 1 procs for 10000 steps with 1 atoms 103 | 104 | Performance: 340024457.059 tau/day, 393546.825 timesteps/s 105 | 92.5% CPU use with 1 MPI tasks x no OpenMP threads 106 | 107 | MPI task timing breakdown: 108 | Section | min time | avg time | max time |%varavg| %total 109 | --------------------------------------------------------------- 110 | Pair | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 1.83 111 | Neigh | 0.015332 | 0.015332 | 0.015332 | 0.0 | 60.34 112 | Comm | 0.0038674 | 0.0038674 | 0.0038674 | 0.0 | 15.22 113 | Output | 0.0023129 | 0.0023129 | 0.0023129 | 0.0 | 9.10 114 | Modify | 0.0018332 | 0.0018332 | 0.0018332 | 0.0 | 7.21 115 | Other | | 0.0016 | | | 6.30 116 | 117 | Nlocal: 1 ave 1 max 1 min 118 | Histogram: 1 0 0 0 0 0 0 0 0 0 119 | Nghost: 0 ave 0 max 0 min 120 | Histogram: 1 0 0 0 0 0 0 0 0 0 121 | Neighs: 0 ave 0 max 0 min 122 | Histogram: 1 0 0 0 0 0 0 0 0 0 123 | 124 | Total # of neighbors = 0 125 | Ave neighs/atom = 0 126 | Neighbor list builds = 123 127 | Dangerous builds = 0 128 | Total wall time: 0:00:00 129 | -------------------------------------------------------------------------------- /lammps_tutorial/plots.gplot: -------------------------------------------------------------------------------- 1 | set term pngcairo enhanced font "Helvetica,14" size 500,300 2 | set output "LJ.png" 3 | 4 | set ylabel "U_{WCA}(r)" 5 | set xlabel "r [{/Symbol s}]" 6 | 7 | lj(x,e,s)=4*e*( (s/x)**12 - (s/x)**6 ) 8 | ljcut(x,e,s,rc) = x 211 220 44 | set group ct type 3 45 | group ct delete 46 | 47 | ### 48 | # Dump configurations 49 | ### 50 | dump dum1 all custom 1000 dump.DNA+proteins id type xs ys zs ix iy iz 51 | # every 1000 time steps, each atom's id, type, x,y,z coords and x,y,z image flages are output. 52 | # image flags count how many times each atom has moved through a periodic boundary 53 | 54 | ### 55 | # Set up interactions - start with 'soft' potentials 56 | ### 57 | 58 | ## angles 59 | angle_style cosine 60 | angle_coeff 1 20.0 61 | # this choice gives a polymer with the same persistence length as DNA 62 | 63 | ## Between bonded atoms 64 | bond_style harmonic 65 | # For style harmonic, specify: 66 | # * bond type 67 | # * K (energy/distance^2) 68 | # * R0 (distance) 69 | bond_coeff 1 90.0 1.1 70 | special_bonds lj 1.0 1.0 1.0 71 | 72 | ## Between non-bonded atoms 73 | pair_style soft 1.12246152962189 74 | # pair_coeff for soft, specify 3: 75 | # * atom type interacting with 76 | # * atom type 77 | # * energy 78 | # * cutoff 79 | pair_coeff 1 1 100.0 1.12246152962189 80 | pair_coeff 1 2 100.0 1.6836922944328352 # lets make the proteins diameter 2 81 | pair_coeff 1 3 100.0 1.6836922944328352 # lets make the proteins diameter 2 82 | pair_coeff 2 2 100.0 2.2449230592437801 83 | pair_coeff 2 3 100.0 2.2449230592437801 84 | pair_coeff 3 3 100.0 2.2449230592437801 85 | 86 | ### 87 | # Set up fixes 88 | ### 89 | variable seed equal 54654651 # a seed for the thermostat 90 | 91 | fix 1 all nve # NVE integrator 92 | fix 2 all langevin 1.0 1.0 1.0 ${seed} # langevin thermostat 93 | 94 | ##### Output thermodynamic info (temperature, energy, pressure, etc.) ##### 95 | thermo 1000 96 | thermo_style custom step temp epair emol press vol 97 | ############################################################################ 98 | 99 | 100 | ##### Output thermodynamic info to file ################################### 101 | variable t equal step 102 | variable mytemp equal temp 103 | variable myepair equal epair 104 | fix mythermofile all print 1000 "$t ${mytemp} ${myepair}" file thermo_output.dat screen no 105 | ############################################################################ 106 | 107 | ############################################################################ 108 | #### Set up a compute for R_g 109 | compute myRG2compute all gyration 110 | #### and write it to a file 111 | variable RG2 equal c_myRG2compute 112 | fix myRG2file all print 1000 "$t ${RG2}" file radius_of_gyration_squared.dat screen no 113 | ############################################################################ 114 | 115 | 116 | 117 | ### 118 | # set timestep of integrator 119 | ### 120 | timestep 0.01 121 | 122 | ### 123 | # run integration for a number of steps to equilibrate with soft potnentials 124 | ### 125 | 126 | run 5000 127 | 128 | write_restart DNA_prot.equlilb.restart 129 | 130 | 131 | ### 132 | # Now switch to LJ potential and FENE bonds 133 | 134 | ## Between bonded atoms 135 | bond_style fene 136 | special_bonds fene #<=== I M P O R T A N T prevents LJ from being counted twice 137 | # For style FENE, specify: 138 | # * bond type 139 | # * K (energy/distance^2) 140 | # * R0 (distance) 141 | # * epsilon 142 | # * sigma 143 | bond_coeff 1 30.0 1.6 1.0 1.0 144 | 145 | ## Between non-bonded atoms 146 | pair_style lj/cut 1.12246152962189 147 | pair_modify shift yes # option to ensure energy is calculated corectly 148 | # pair_coeff for LJ, specify 4: 149 | # * atom type interacting with 150 | # * atom type 151 | # * energy 152 | # * mean diameter of the two atom types 153 | # * cutoff 154 | pair_coeff 1 1 1.0 1.0 1.12246152962189 155 | pair_coeff 1 2 1.0 1.5 1.6836922944328352 156 | pair_coeff 1 3 1.0 1.5 1.6836922944328352 157 | pair_coeff 2 2 1.0 2.0 2.2449230592437801 158 | pair_coeff 2 3 1.0 2.0 2.2449230592437801 159 | pair_coeff 3 3 1.0 2.0 2.2449230592437801 160 | # here we have set the diameter of the proteins to 2 161 | # the interaction diameter between DNA and proteins is the mean of their diameters 162 | # we have chosen the cut off at the minimum of the potential -- there is no attractive part 163 | 164 | 165 | ### 166 | # now do a longer run with no attractive interactions 167 | ### 168 | 169 | run 100000 170 | 171 | ### 172 | # switch on attraction between protein type 2 and DNA 173 | ### 174 | pair_coeff 1 2 5.0 1.5 2.5 175 | # we have increased the cut off, and chosen an interaction energy of 5k_BT 176 | 177 | ## do a run with switching 178 | 179 | # lets have a switching rate of 1/50000 steps 180 | variable switchrate equal 1.0/50000 181 | # lets attempt to switch every 1000 182 | variable switchsteps equal 1000 183 | # and run for a total of 184 | variable maxsteps equal 5000000 185 | variable switches equal ceil(${maxsteps}/${switchsteps}) 186 | 187 | # so at every attempt, this many will switch on average 188 | variable fracswitching equal ${switchrate}*${switchsteps} 189 | 190 | # get a rand seed each time 191 | variable switchseed equal floor(random(1000,99999,5415465)) 192 | 193 | 194 | variable a loop ${switches} 195 | label swloop # start of loop 196 | 197 | group spheres_on type 2 198 | group spheres_off type 3 199 | # type 2 switches to type 3 200 | set group spheres_on type/fraction 3 ${fracswitching} ${switchseed} 201 | # and type 3 switches to type 2 202 | set group spheres_off type/fraction 2 ${fracswitching} ${switchseed} 203 | group spheres_on delete 204 | group spheres_off delete 205 | 206 | run ${switchsteps} 207 | 208 | next a 209 | jump SELF swloop # end of loop 210 | 211 | 212 | 213 | 214 | #### write a final restart file 215 | write_restart final.restart -------------------------------------------------------------------------------- /lammps_tutorial/tutorial5/polymer_plus_bridges.lam: -------------------------------------------------------------------------------- 1 | ############################################### 2 | # LAMMPS script for a DNA and proteins 3 | ############################################### 4 | 5 | ### 6 | # Box and units (use LJ units and periodic boundaries) 7 | ### 8 | 9 | units lj # use lennard-jones (i.e. dimensionless) units 10 | atom_style angle # atoms with bonds and angles 11 | 12 | boundary p p p # all boundaries are periodic 13 | 14 | ### 15 | # Pair interactions require lists of neighbours to be calculated 16 | ### 17 | neighbor 1.9 bin 18 | neigh_modify every 1 delay 1 check yes 19 | 20 | 21 | ### 22 | # READ "start" data file 23 | ### 24 | read_data initial_configuration.txt 25 | 26 | 27 | ### 28 | # Reset timestep 29 | ### 30 | reset_timestep 0 31 | 32 | ### 33 | # Define groups 34 | ### 35 | group all type 1 2 36 | group dna type 1 37 | group prot type 2 38 | 39 | ### 40 | # Dump configurations 41 | ### 42 | dump dum1 all custom 1000 dump.DNA+proteins id type xs ys zs ix iy iz 43 | # every 1000 time steps, each atom's id, type, x,y,z coords and x,y,z image flages are output. 44 | # image flags count how many times each atom has moved through a periodic boundary 45 | 46 | ### 47 | # Set up interactions - start with 'soft' potentials 48 | ### 49 | 50 | ## angles 51 | angle_style cosine 52 | angle_coeff 1 20.0 53 | # this choice gives a polymer with the same persistence length as DNA 54 | 55 | ## Between bonded atoms 56 | bond_style harmonic 57 | # For style harmonic, specify: 58 | # * bond type 59 | # * K (energy/distance^2) 60 | # * R0 (distance) 61 | bond_coeff 1 90.0 1.1 62 | 63 | 64 | ## Between non-bonded atoms 65 | pair_style soft 1.12246152962189 66 | # pair_coeff for soft, specify 3: 67 | # * atom type interacting with 68 | # * atom type 69 | # * energy 70 | # * cutoff 71 | pair_coeff 1 1 100.0 1.12246152962189 72 | pair_coeff 1 2 100.0 1.6836922944328352 # lets make the proteins diameter 2 73 | pair_coeff 2 2 100.0 2.2449230592437801 74 | 75 | ### 76 | # Set up fixes 77 | ### 78 | variable seed equal 54654651 # a seed for the thermostat 79 | 80 | fix 1 all nve # NVE integrator 81 | fix 2 all langevin 1.0 1.0 1.0 ${seed} # langevin thermostat 82 | 83 | ##### Output thermodynamic info (temperature, energy, pressure, etc.) ##### 84 | thermo 1000 85 | thermo_style custom step temp epair emol press vol 86 | ############################################################################ 87 | 88 | 89 | ##### Output thermodynamic info to file ################################### 90 | variable t equal step 91 | variable mytemp equal temp 92 | variable myepair equal epair 93 | fix mythermofile all print 1000 "$t ${mytemp} ${myepair}" file thermo_output.dat screen no 94 | ############################################################################ 95 | 96 | ############################################################################ 97 | #### Set up a compute for R_g 98 | compute myRG2compute all gyration 99 | #### and write it to a file 100 | variable RG2 equal c_myRG2compute 101 | fix myRG2file all print 1000 "$t ${RG2}" file radius_of_gyration_squared.dat screen no 102 | ############################################################################ 103 | 104 | 105 | 106 | ### 107 | # set timestep of integrator 108 | ### 109 | timestep 0.01 110 | 111 | ### 112 | # run integration for a number of steps to equilibrate with soft potnentials 113 | ### 114 | 115 | run 5000 116 | 117 | write_restart DNA_prot.equlilb.restart 118 | 119 | 120 | ### 121 | # Now switch to LJ potential and FENE bonds 122 | 123 | ## Between bonded atoms 124 | bond_style fene 125 | special_bonds fene #<=== I M P O R T A N T prevents LJ from being counted twice 126 | # For style FENE, specify: 127 | # * bond type 128 | # * K (energy/distance^2) 129 | # * R0 (distance) 130 | # * epsilon 131 | # * sigma 132 | bond_coeff 1 30.0 1.6 1.0 1.0 133 | 134 | ## Between non-bonded atoms 135 | pair_style lj/cut 1.12246152962189 136 | pair_modify shift yes # option to ensure energy is calculated corectly 137 | # pair_coeff for LJ, specify 4: 138 | # * atom type interacting with 139 | # * atom type 140 | # * energy 141 | # * mean diameter of the two atom types 142 | # * cutoff 143 | pair_coeff 1 1 1.0 1.0 1.12246152962189 144 | pair_coeff 1 2 1.0 1.5 1.6836922944328352 145 | pair_coeff 2 2 1.0 2.0 2.2449230592437801 146 | # here we have set the diameter of the proteins to 2 147 | # the interaction diameter between DNA and proteins is the mean of their diameters 148 | # we have chosen the cut off at the minimum of the potential -- there is no attractive part 149 | 150 | 151 | ### 152 | # now do a longer run with no attractive interactions 153 | ### 154 | 155 | run 100000 156 | 157 | ### 158 | # switch on attraction between proteins and DNA 159 | ### 160 | pair_coeff 1 2 5.0 1.5 2.5 161 | # we have increased the cut off, and chosen an interaction energy of 5k_BT 162 | 163 | ## do another run 164 | run 200000 165 | 166 | 167 | #### write a final restart file 168 | write_restart final.restart -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/README: -------------------------------------------------------------------------------- 1 | 2 | 3 | c++ ~/work/scripts_for_students/lammps/generate_gridDNA.cc -o generate_DNA 4 | ./generate_DNA 5 | 100 6 | 60 7 | 60 8 | 60 9 | 46454 10 | 11 | 12 | ~/work/lmp-7Dec15_openmpi_SL7 < in.twistDNA_1stequilib 13 | 14 | 15 | c++ ~/work/DNAmodels/ellipsoids/tools/measure_linking_loop.cc -O3 -o measure_linking 16 | 17 | ./measure_linking dump_1stequilib.DNA linking_1stequilib.dat 18 | 19 | # This showed that the loop had Tw=1 and Wr=-1 at the end of the simulation. 20 | # For this tutorial, I wanted an unwrithed loop, so I add another equilibration step where I increase the bending energy - should open into a circular loop 21 | 22 | ~/work/lmp-7Dec15_openmpi_SL7 < in.twistDNA_2ndequilib 23 | 24 | 25 | # Now need to convert the restart to an lammps data file with ellipsoids 26 | 27 | ./lammps_restart2data_with_ellipsoids.sh restart.2ndequilib equilibrated_loops.data 28 | 29 | 30 | # Now add some twists 31 | 32 | c++ ~/work/DNAmodels/ellipsoids/tools/add_linking.cc -O3 -o add_links 33 | ./add_links equilibrated_loops.data initial_configuration.txt -4 34 | 35 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/a.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/tutorial6/setup/a.out -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/add_links: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/tutorial6/setup/add_links -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/equilibrated_loops.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 7 Dec 2015, timestep = 100000 2 | 3 | 100 atoms 4 | 100 ellipsoids 5 | 1 atom types 6 | 100 bonds 7 | 1 bond types 8 | 200 angles 9 | 2 angle types 10 | 11 | -3.0000000000000000e+01 3.0000000000000000e+01 xlo xhi 12 | -3.0000000000000000e+01 3.0000000000000000e+01 ylo yhi 13 | -3.0000000000000000e+01 3.0000000000000000e+01 zlo zhi 14 | 15 | Masses 16 | 17 | 1 1 18 | 19 | Atoms # hybrid 20 | 21 | 18 1 6.9577687866770521e+00 -9.6930627245386383e+00 -1.5757128021968612e+01 1 1 1.9098599999999999e+00 0 0 0 22 | 19 1 6.4628850689074149e+00 -8.8470268770987914e+00 -1.5911740674483182e+01 1 1 1.9098599999999999e+00 0 0 0 23 | 20 1 5.9575358167282308e+00 -8.0076911275407365e+00 -1.6027828446360790e+01 1 1 1.9098599999999999e+00 0 0 0 24 | 22 1 4.7471825349646410e+00 -6.4421991652963495e+00 -1.5934175063223437e+01 1 1 1.9098599999999999e+00 0 0 0 25 | 21 1 5.3901962419028076e+00 -7.1152777887795402e+00 -1.6109790541474187e+01 1 1 1.9098599999999999e+00 0 0 0 26 | 17 1 7.3467286168253514e+00 -1.0480434897230872e+01 -1.5387255851396779e+01 1 1 1.9098599999999999e+00 0 0 0 27 | 23 1 4.0905552145504682e+00 -5.7376070731230095e+00 -1.5504894762681330e+01 1 1 1.9098599999999999e+00 0 0 0 28 | 24 1 3.5510834669387727e+00 -5.0257507904569998e+00 -1.5050965260897531e+01 1 1 1.9098599999999999e+00 0 0 0 29 | 15 1 7.9662647675569254e+00 -1.2220027243740910e+01 -1.4586468648764754e+01 1 1 1.9098599999999999e+00 0 0 0 30 | 16 1 7.6177801757067005e+00 -1.1436269895771437e+01 -1.4973617841529467e+01 1 1 1.9098599999999999e+00 0 0 0 31 | 25 1 2.8880982083496121e+00 -4.3965339184668304e+00 -1.4682502887208569e+01 1 1 1.9098599999999999e+00 0 0 0 32 | 14 1 8.3831536976963381e+00 -1.2932565251486190e+01 -1.4055285060018443e+01 1 1 1.9098599999999999e+00 0 0 0 33 | 26 1 2.2272523194469995e+00 -3.7447307818110001e+00 -1.4271466550086510e+01 1 1 1.9098599999999999e+00 0 0 0 34 | 27 1 1.5282050759962860e+00 -3.3164814654093151e+00 -1.3667641269853384e+01 1 1 1.9098599999999999e+00 0 0 0 35 | 12 1 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2.2761684785041927e-01 181 | 46 -0.0162128 -0.343681 -0.344862 -1.4961001122297846e-01 3.2502141248198357e-01 -3.3400393196289108e-01 182 | 88 -0.403027 -1.0402 0.722474 3.7542417648055115e-01 -1.8561135516187544e-01 2.0027902280170445e-01 183 | 47 -1.72869 -0.601158 0.363317 -2.9554231362121852e-01 7.5087237841896048e-01 -5.9187071760122234e-01 184 | 87 0.0671279 -1.38026 -0.438665 2.2342761122197755e-02 2.3137326961648025e-01 1.1081295780662553e-01 185 | 86 -0.953314 -0.144363 -1.75254 5.0023960869362760e-01 -1.4505238696277242e-01 -4.8481942138841938e-01 186 | 48 -1.29239 0.460104 1.46772 7.2314012981098824e-03 -4.4621098859332392e-01 -4.4440422463194976e-02 187 | 85 0.0183816 -0.204763 0.324392 -2.7574272158665564e-01 5.4201038591579487e-02 -1.9989642413140662e-02 188 | 49 -0.276498 1.43868 -0.235393 -9.9714538618015602e-02 -1.0314253846870389e-02 -2.3207170178949024e-01 189 | 50 0.339692 0.478805 -0.224159 2.3167434830696554e-01 -8.2703642713162318e-01 1.1991851229191844e-01 190 | 84 -1.66175 1.24747 1.24478 -4.7898843365230970e-01 -2.2255671848031655e-01 -2.9922220204730826e-01 191 | 51 0.577701 1.02441 -1.26343 -4.7789880387921191e-01 3.7396611840198948e-02 -2.6488046620845401e-01 192 | 83 -0.317973 -0.814523 -0.265992 1.4877196661549835e-01 -9.2512194035168194e-02 2.7777033866273204e-01 193 | 52 0.434167 0.122439 0.793184 3.2188516811027440e-01 -1.5669000416018941e-01 -7.5650440962815180e-01 194 | 82 -0.579042 -0.389035 -1.11249 1.5982396612020483e-01 1.7900788376859905e-01 1.5188825110078799e-01 195 | 53 -0.753876 -0.292685 1.82955 3.2312212412627561e-01 1.8832733955259032e-01 6.0891464833913100e-01 196 | 81 0.547684 0.418362 0.0312104 2.6175076452901747e-01 -1.7795277050951713e-02 5.1835064482525295e-01 197 | 54 0.106587 0.0625046 -0.529421 -6.4224887470458292e-02 4.6568968945118715e-02 -4.6332356292073856e-02 198 | 56 0.914678 -1.27813 0.771782 -2.6421259996647672e-01 4.8353803171636056e-01 -2.7645552417575642e-01 199 | 57 -1.815 -0.106232 -0.608356 -4.2815723285208773e-02 -6.6217540710606193e-01 -3.8169033039393907e-01 200 | 55 -1.98978 0.599832 -0.499373 -2.8675415265597116e-02 4.1740226226533694e-01 -3.0729429309074484e-02 201 | 80 -0.448244 0.371495 1.25376 -6.6429799404875378e-01 3.0805119055189284e-01 -4.1153043181030696e-01 202 | 63 1.05216 -1.35749 -2.33738 2.5168068910168617e-01 -1.9592830567338715e-01 1.1710767424867478e-01 203 | 62 1.2197 0.323953 -0.313541 -1.5302312679245009e-01 2.1679011195172562e-01 -2.5976755443534111e-01 204 | 61 1.04923 -1.04602 1.35608 6.8641174236690439e-01 1.6771939053597626e-02 -1.3325372903210023e-01 205 | 60 1.13645 -1.40235 0.069657 -2.6948027730095298e-01 -2.1646689964727972e-01 -1.6296555565149229e-01 206 | 58 -0.226783 -0.41978 0.634262 3.3570735126495910e-01 -1.0205903688176612e-01 -1.8611814183681791e-01 207 | 59 0.746523 -0.285916 -0.535436 5.2580905702059066e-01 -4.4644646613884265e-01 -1.5783395402067962e-01 208 | 79 0.609948 1.67877 -0.206553 1.4439647848808568e-01 -9.1552254229854538e-02 6.2699009995497190e-01 209 | 65 -1.45453 -0.160838 0.748597 -6.0244361378924305e-02 3.4564456261228849e-01 -5.4793479768911291e-01 210 | 64 -0.738807 0.181935 -0.8745 -4.8655625575255053e-02 -4.3907307221479459e-02 -4.7380259992475970e-01 211 | 78 1.42996 -0.877694 0.0909594 2.8392901716566993e-01 2.6434715389254820e-01 7.3752167642703453e-02 212 | 66 -0.667251 -0.678196 0.95907 1.2349983251973323e-01 1.4477172149669959e-01 9.4066601127859972e-02 213 | 67 1.10749 -0.575159 0.523222 -1.1220623405954225e-01 -1.8874538452049583e-01 2.7681713264605179e-01 214 | 77 0.142234 -0.615016 -1.00383 1.7230376887196047e-01 -3.3491465241483981e-01 -4.8804412164425243e-01 215 | 76 1.49438 0.732355 -0.118232 -2.1974478591055061e-01 -4.0289533015900381e-01 -2.1275844163431687e-01 216 | 68 1.44277 -1.16431 -0.502277 -1.1227699055615491e-01 5.4683716125120096e-01 -3.2280778387638487e-02 217 | 75 0.655192 0.364674 -0.710413 1.3179952156950972e-01 2.2634798837710385e-01 -1.5742679271917262e-02 218 | 74 -1.29039 -1.29351 0.752284 4.8280079021414113e-01 -4.8605924120962590e-01 3.1559123368874775e-01 219 | 73 -0.715784 0.0408448 -0.662993 3.1679841408202888e-02 2.2310309135601722e-01 -4.2122433107639701e-01 220 | 72 -1.98125 -0.592565 0.52424 -2.1301665162735586e-01 2.2922816232489363e-01 1.0242521411194930e-01 221 | 70 0.568691 -1.15431 0.341076 -8.1051241283483330e-02 2.0117359004473159e-01 -1.7007333480701955e-01 222 | 71 0.557168 -1.57877 0.777848 2.5314778903405566e-01 2.0647164021617523e-02 -9.0395667643862157e-02 223 | 69 -0.172044 -0.503975 -0.704695 -1.0503297022883343e-01 9.4743732088312702e-02 -9.5619972238938339e-02 224 | 225 | Bonds 226 | 227 | 1 1 18 19 228 | 2 1 19 20 229 | 3 1 20 21 230 | 4 1 22 23 231 | 5 1 21 22 232 | 6 1 17 18 233 | 7 1 23 24 234 | 8 1 24 25 235 | 9 1 15 16 236 | 10 1 16 17 237 | 11 1 25 26 238 | 12 1 14 15 239 | 13 1 26 27 240 | 14 1 27 28 241 | 15 1 12 13 242 | 16 1 13 14 243 | 17 1 28 29 244 | 18 1 11 12 245 | 19 1 10 11 246 | 20 1 29 30 247 | 21 1 9 10 248 | 22 1 30 31 249 | 23 1 8 9 250 | 24 1 7 8 251 | 25 1 31 32 252 | 26 1 6 7 253 | 27 1 32 33 254 | 28 1 5 6 255 | 29 1 33 34 256 | 30 1 4 5 257 | 31 1 34 35 258 | 32 1 3 4 259 | 33 1 2 3 260 | 34 1 1 2 261 | 35 1 35 36 262 | 36 1 100 1 263 | 37 1 36 37 264 | 38 1 99 100 265 | 39 1 37 38 266 | 40 1 98 99 267 | 41 1 97 98 268 | 42 1 38 39 269 | 43 1 96 97 270 | 44 1 39 40 271 | 45 1 95 96 272 | 46 1 40 41 273 | 47 1 94 95 274 | 48 1 41 42 275 | 49 1 93 94 276 | 50 1 42 43 277 | 51 1 92 93 278 | 52 1 43 44 279 | 53 1 91 92 280 | 54 1 90 91 281 | 55 1 44 45 282 | 56 1 45 46 283 | 57 1 89 90 284 | 58 1 46 47 285 | 59 1 88 89 286 | 60 1 47 48 287 | 61 1 87 88 288 | 62 1 86 87 289 | 63 1 48 49 290 | 64 1 85 86 291 | 65 1 49 50 292 | 66 1 50 51 293 | 67 1 84 85 294 | 68 1 51 52 295 | 69 1 83 84 296 | 70 1 52 53 297 | 71 1 82 83 298 | 72 1 53 54 299 | 73 1 81 82 300 | 74 1 54 55 301 | 75 1 56 57 302 | 76 1 57 58 303 | 77 1 55 56 304 | 78 1 80 81 305 | 79 1 63 64 306 | 80 1 62 63 307 | 81 1 61 62 308 | 82 1 60 61 309 | 83 1 58 59 310 | 84 1 59 60 311 | 85 1 79 80 312 | 86 1 65 66 313 | 87 1 64 65 314 | 88 1 78 79 315 | 89 1 66 67 316 | 90 1 67 68 317 | 91 1 77 78 318 | 92 1 76 77 319 | 93 1 68 69 320 | 94 1 75 76 321 | 95 1 74 75 322 | 96 1 73 74 323 | 97 1 72 73 324 | 98 1 70 71 325 | 99 1 71 72 326 | 100 1 69 70 327 | 328 | Angles 329 | 330 | 1 2 17 18 18 331 | 2 1 17 18 19 332 | 3 2 18 19 19 333 | 4 1 18 19 20 334 | 5 2 19 20 20 335 | 6 1 19 20 21 336 | 7 2 21 22 22 337 | 8 1 21 22 23 338 | 9 2 20 21 21 339 | 10 1 20 21 22 340 | 11 2 16 17 17 341 | 12 1 16 17 18 342 | 13 2 22 23 23 343 | 14 1 22 23 24 344 | 15 2 23 24 24 345 | 16 1 23 24 25 346 | 17 2 14 15 15 347 | 18 1 14 15 16 348 | 19 2 15 16 16 349 | 20 1 15 16 17 350 | 21 2 24 25 25 351 | 22 1 24 25 26 352 | 23 2 13 14 14 353 | 24 1 13 14 15 354 | 25 2 25 26 26 355 | 26 1 25 26 27 356 | 27 2 26 27 27 357 | 28 1 26 27 28 358 | 29 2 11 12 12 359 | 30 1 11 12 13 360 | 31 2 12 13 13 361 | 32 1 12 13 14 362 | 33 2 27 28 28 363 | 34 1 27 28 29 364 | 35 2 10 11 11 365 | 36 1 10 11 12 366 | 37 2 9 10 10 367 | 38 1 9 10 11 368 | 39 2 28 29 29 369 | 40 1 28 29 30 370 | 41 2 8 9 9 371 | 42 1 8 9 10 372 | 43 2 29 30 30 373 | 44 1 29 30 31 374 | 45 2 7 8 8 375 | 46 1 7 8 9 376 | 47 2 6 7 7 377 | 48 1 6 7 8 378 | 49 2 30 31 31 379 | 50 1 30 31 32 380 | 51 2 5 6 6 381 | 52 1 5 6 7 382 | 53 2 31 32 32 383 | 54 1 31 32 33 384 | 55 2 4 5 5 385 | 56 1 4 5 6 386 | 57 2 32 33 33 387 | 58 1 32 33 34 388 | 59 2 3 4 4 389 | 60 1 3 4 5 390 | 61 2 33 34 34 391 | 62 1 33 34 35 392 | 63 2 2 3 3 393 | 64 1 2 3 4 394 | 65 2 1 2 2 395 | 66 1 1 2 3 396 | 67 1 100 1 2 397 | 68 2 100 1 1 398 | 69 2 34 35 35 399 | 70 1 34 35 36 400 | 71 2 99 100 100 401 | 72 1 99 100 1 402 | 73 2 35 36 36 403 | 74 1 35 36 37 404 | 75 2 98 99 99 405 | 76 1 98 99 100 406 | 77 2 36 37 37 407 | 78 1 36 37 38 408 | 79 2 97 98 98 409 | 80 1 97 98 99 410 | 81 2 96 97 97 411 | 82 1 96 97 98 412 | 83 2 37 38 38 413 | 84 1 37 38 39 414 | 85 2 95 96 96 415 | 86 1 95 96 97 416 | 87 2 38 39 39 417 | 88 1 38 39 40 418 | 89 2 94 95 95 419 | 90 1 94 95 96 420 | 91 2 39 40 40 421 | 92 1 39 40 41 422 | 93 2 93 94 94 423 | 94 1 93 94 95 424 | 95 2 40 41 41 425 | 96 1 40 41 42 426 | 97 2 92 93 93 427 | 98 1 92 93 94 428 | 99 2 41 42 42 429 | 100 1 41 42 43 430 | 101 2 91 92 92 431 | 102 1 91 92 93 432 | 103 2 42 43 43 433 | 104 1 42 43 44 434 | 105 2 90 91 91 435 | 106 1 90 91 92 436 | 107 2 89 90 90 437 | 108 1 89 90 91 438 | 109 2 43 44 44 439 | 110 1 43 44 45 440 | 111 2 44 45 45 441 | 112 1 44 45 46 442 | 113 2 88 89 89 443 | 114 1 88 89 90 444 | 115 2 45 46 46 445 | 116 1 45 46 47 446 | 117 2 87 88 88 447 | 118 1 87 88 89 448 | 119 2 46 47 47 449 | 120 1 46 47 48 450 | 121 2 86 87 87 451 | 122 1 86 87 88 452 | 123 2 85 86 86 453 | 124 1 85 86 87 454 | 125 2 47 48 48 455 | 126 1 47 48 49 456 | 127 2 84 85 85 457 | 128 1 84 85 86 458 | 129 2 48 49 49 459 | 130 1 48 49 50 460 | 131 2 49 50 50 461 | 132 1 49 50 51 462 | 133 2 83 84 84 463 | 134 1 83 84 85 464 | 135 2 50 51 51 465 | 136 1 50 51 52 466 | 137 2 82 83 83 467 | 138 1 82 83 84 468 | 139 2 51 52 52 469 | 140 1 51 52 53 470 | 141 2 81 82 82 471 | 142 1 81 82 83 472 | 143 2 52 53 53 473 | 144 1 52 53 54 474 | 145 2 80 81 81 475 | 146 1 80 81 82 476 | 147 2 53 54 54 477 | 148 1 53 54 55 478 | 149 2 55 56 56 479 | 150 1 55 56 57 480 | 151 2 56 57 57 481 | 152 1 56 57 58 482 | 153 2 54 55 55 483 | 154 1 54 55 56 484 | 155 2 79 80 80 485 | 156 1 79 80 81 486 | 157 2 62 63 63 487 | 158 1 62 63 64 488 | 159 2 61 62 62 489 | 160 1 61 62 63 490 | 161 2 60 61 61 491 | 162 1 60 61 62 492 | 163 2 59 60 60 493 | 164 1 59 60 61 494 | 165 2 57 58 58 495 | 166 1 57 58 59 496 | 167 2 58 59 59 497 | 168 1 58 59 60 498 | 169 2 78 79 79 499 | 170 1 78 79 80 500 | 171 2 64 65 65 501 | 172 1 64 65 66 502 | 173 2 63 64 64 503 | 174 1 63 64 65 504 | 175 2 77 78 78 505 | 176 1 77 78 79 506 | 177 2 65 66 66 507 | 178 1 65 66 67 508 | 179 2 66 67 67 509 | 180 1 66 67 68 510 | 181 2 76 77 77 511 | 182 1 76 77 78 512 | 183 2 75 76 76 513 | 184 1 75 76 77 514 | 185 2 67 68 68 515 | 186 1 67 68 69 516 | 187 2 74 75 75 517 | 188 1 74 75 76 518 | 189 2 73 74 74 519 | 190 1 73 74 75 520 | 191 2 72 73 73 521 | 192 1 72 73 74 522 | 193 2 71 72 72 523 | 194 1 71 72 73 524 | 195 2 69 70 70 525 | 196 1 69 70 71 526 | 197 2 70 71 71 527 | 198 1 70 71 72 528 | 199 2 68 69 69 529 | 200 1 68 69 70 530 | 531 | Ellipsoids 532 | 533 | 18 1 1 1 0.5063 -0.230908 -0.73747 -0.382726 534 | 19 1 1 1 0.502544 -0.212524 -0.729258 -0.412876 535 | 20 1 1 1 0.534599 -0.220281 -0.693947 -0.42909 536 | 22 1 1 1 0.780039 -0.121662 -0.520759 -0.32488 537 | 21 1 1 1 0.623648 -0.17802 -0.670866 -0.359598 538 | 17 1 1 1 0.416759 -0.230186 -0.813759 -0.333351 539 | 23 1 1 1 0.732949 -0.34413 -0.526237 -0.259681 540 | 24 1 1 1 0.793754 -0.317657 -0.424019 -0.298759 541 | 15 1 1 1 0.345416 -0.201613 -0.825751 -0.397713 542 | 16 1 1 1 0.34886 -0.239811 -0.795872 -0.432869 543 | 25 1 1 1 0.781695 -0.208469 -0.515613 -0.282199 544 | 14 1 1 1 0.241332 -0.305719 -0.860103 -0.32942 545 | 26 1 1 1 0.784061 -0.0776437 -0.463195 -0.405796 546 | 27 1 1 1 0.874128 0.0633926 -0.330222 -0.350479 547 | 12 1 1 1 0.18412 -0.297125 -0.877782 -0.327589 548 | 13 1 1 1 0.266159 -0.322605 -0.872037 -0.254239 549 | 28 1 1 1 0.808612 -0.170371 -0.116409 -0.550972 550 | 11 1 1 1 0.182584 -0.328004 -0.83747 -0.397139 551 | 10 1 1 1 0.138198 -0.373199 -0.879909 -0.259584 552 | 29 1 1 1 0.747745 -0.0404795 0.0371108 -0.661711 553 | 9 1 1 1 0.154785 -0.236753 -0.899666 -0.332553 554 | 30 1 1 1 0.74854 -0.148188 -0.121497 -0.634797 555 | 8 1 1 1 0.104956 -0.293552 -0.912056 -0.266392 556 | 7 1 1 1 0.371449 -0.191426 -0.90326 -0.0974824 557 | 31 1 1 1 0.786002 -0.039339 0.00297062 -0.616963 558 | 6 1 1 1 0.323541 -0.298219 -0.888175 -0.132405 559 | 32 1 1 1 0.711325 -0.00806072 0.074195 -0.69889 560 | 5 1 1 1 0.363245 -0.269853 -0.888656 -0.0743175 561 | 33 1 1 1 0.681634 0.0795397 -0.0485552 -0.725735 562 | 4 1 1 1 0.276149 -0.30706 -0.883107 -0.222663 563 | 34 1 1 1 0.784723 -0.0522444 0.187545 -0.588479 564 | 3 1 1 1 0.390428 -0.186526 -0.899717 -0.0573092 565 | 2 1 1 1 0.363785 -0.179007 -0.90839 -0.102199 566 | 1 1 1 1 0.569316 -0.159842 -0.804753 -0.0519934 567 | 35 1 1 1 0.823 0.0503597 0.0754504 -0.560752 568 | 100 1 1 1 0.342594 -0.36308 -0.851862 -0.158532 569 | 36 1 1 1 0.804935 0.0138817 0.105334 -0.583773 570 | 99 1 1 1 0.524039 -0.230282 -0.817165 -0.0677931 571 | 37 1 1 1 0.839491 0.0355764 0.162725 -0.517214 572 | 98 1 1 1 0.431408 -0.152501 -0.883632 -0.099123 573 | 97 1 1 1 0.386807 -0.326383 -0.859605 -0.0702404 574 | 38 1 1 1 0.777013 0.151863 0.327437 -0.515726 575 | 96 1 1 1 0.348332 -0.281025 -0.892412 -0.0573577 576 | 39 1 1 1 0.739799 0.0253323 0.314575 -0.594221 577 | 95 1 1 1 0.412728 -0.25405 -0.866466 0.119797 578 | 40 1 1 1 0.813649 -0.0643605 0.267841 -0.511952 579 | 94 1 1 1 0.349526 -0.269125 -0.885579 0.145439 580 | 41 1 1 1 0.767811 0.0658994 0.281867 -0.571555 581 | 93 1 1 1 0.404688 -0.337579 -0.84985 0.00488308 582 | 42 1 1 1 0.729309 -0.0219325 0.333605 -0.596938 583 | 92 1 1 1 0.298199 -0.461081 -0.82647 0.12421 584 | 43 1 1 1 0.698984 -0.129656 0.196641 -0.675236 585 | 91 1 1 1 -0.210821 0.50178 0.835748 -0.0727787 586 | 90 1 1 1 -0.160205 0.352133 0.920472 0.0553844 587 | 44 1 1 1 0.692732 -0.0436318 0.139371 -0.706254 588 | 45 1 1 1 0.601942 0.0395625 0.178721 -0.777277 589 | 89 1 1 1 -0.16965 0.399131 0.900926 -0.01567 590 | 46 1 1 1 0.680432 -0.0547892 0.114481 -0.721737 591 | 88 1 1 1 -0.296578 0.459354 0.802159 -0.23995 592 | 47 1 1 1 0.676954 0.0845223 0.152907 -0.714988 593 | 87 1 1 1 -0.337519 0.456566 0.823073 -0.0133671 594 | 86 1 1 1 -0.228942 0.495639 0.837693 -0.0140559 595 | 48 1 1 1 0.755328 -0.139044 0.198405 -0.608918 596 | 85 1 1 1 0.0705124 0.474478 0.873303 0.0850905 597 | 49 1 1 1 0.66269 -0.24592 0.101825 -0.699998 598 | 50 1 1 1 0.68249 -0.264695 0.2054 -0.649581 599 | 84 1 1 1 -0.00686612 0.514377 0.841709 -0.164001 600 | 51 1 1 1 0.627869 -0.159856 0.383464 -0.658165 601 | 83 1 1 1 -0.00637639 0.522387 0.838902 -0.152692 602 | 52 1 1 1 0.821305 -0.178794 0.280989 -0.463181 603 | 82 1 1 1 0.0642359 0.475801 0.849328 -0.219384 604 | 53 1 1 1 0.848933 -0.0867695 0.340741 -0.394562 605 | 81 1 1 1 -0.0511101 0.505862 0.817608 -0.270203 606 | 54 1 1 1 0.857294 -0.0992221 0.426479 -0.270773 607 | 56 1 1 1 0.715098 0.0150672 0.65684 -0.238683 608 | 57 1 1 1 0.62043 -0.019319 0.635421 -0.459274 609 | 55 1 1 1 0.817951 -0.0199135 0.527294 -0.229176 610 | 80 1 1 1 0.0397356 0.441397 0.861493 -0.247832 611 | 63 1 1 1 0.63741 0.16645 0.642596 -0.391245 612 | 62 1 1 1 0.679764 0.0904035 0.572838 -0.449003 613 | 61 1 1 1 0.559246 -0.00491914 0.710146 -0.427682 614 | 60 1 1 1 0.469339 -0.00961176 0.84208 -0.265574 615 | 58 1 1 1 0.635776 -0.0557722 0.727388 -0.252162 616 | 59 1 1 1 0.629727 -0.0891723 0.703712 -0.316674 617 | 79 1 1 1 0.133086 0.482011 0.829883 -0.247484 618 | 65 1 1 1 0.733321 0.296594 0.503666 -0.347265 619 | 64 1 1 1 0.753134 0.179898 0.556856 -0.300562 620 | 78 1 1 1 0.127774 0.394213 0.870733 -0.264751 621 | 66 1 1 1 0.771382 0.218295 0.486155 -0.347808 622 | 67 1 1 1 0.765853 0.14395 0.39859 -0.483605 623 | 77 1 1 1 0.174914 0.25607 0.840167 -0.444918 624 | 76 1 1 1 0.215544 0.344897 0.833491 -0.374005 625 | 68 1 1 1 0.834582 0.0489643 0.457084 -0.303563 626 | 75 1 1 1 0.368827 0.277811 0.753139 -0.468582 627 | 74 1 1 1 0.40118 0.192421 0.727117 -0.522809 628 | 73 1 1 1 0.393666 0.139114 0.742864 -0.523286 629 | 72 1 1 1 0.563743 0.0901571 0.670855 -0.473305 630 | 70 1 1 1 0.599784 0.0636623 0.765019 -0.225724 631 | 71 1 1 1 0.511615 0.0795306 0.76456 -0.383893 632 | 69 1 1 1 0.815557 0.0949401 0.493918 -0.286177 633 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/in.twistDNA_1stequilib: -------------------------------------------------------------------------------- 1 | 2 | ### 3 | # Box and units (use LJ units and periodic boundaries) 4 | ### 5 | 6 | units lj 7 | 8 | atom_style hybrid angle ellipsoid 9 | 10 | boundary p p p 11 | 12 | ### 13 | # Pair interactions require lists of neighbours to be calculated 14 | ### 15 | neighbor 1.9 bin 16 | neigh_modify every 1 delay 1 check yes 17 | 18 | ### Generate RESTART file, SPECIAL format, not a .txt file ### 19 | ### Use this as initial configurations ### 20 | #restart 2000000 DNA.${run}.restart 21 | ############################# 22 | 23 | #processors 2 1 1 24 | 25 | ### READ "start" data file ### 26 | read_data lammps.input 27 | ###################### 28 | 29 | ###################### 30 | ### reset timestep ### 31 | reset_timestep 0 32 | ###################### 33 | 34 | ### 35 | # Define groups (atom type 1 is group 'all') 36 | ### 37 | group all type 1 38 | 39 | ### 40 | # Dump configs 41 | ### 42 | 43 | # A dump file with bead orientations 44 | compute quat all property/atom quatw quati quatj quatk 45 | dump d2 all custom 1000 dump_1stequilib.DNA id type xs ys zs ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] 46 | 47 | ################################################################### 48 | # Stiffness term 49 | # 50 | # E = K * (1+cos(theta)), K>0 51 | # 52 | angle_style hybrid cosine polytorsion 53 | angle_coeff 1 cosine 20.0 54 | angle_coeff 2 polytorsion 70.0 30.0 55 | 56 | ################################################################### 57 | 58 | ### 59 | # Start off with soft potentials 60 | ### 61 | 62 | ################################################################### 63 | # Pair interaction between non-bonded atoms 64 | 65 | pair_style soft 1.12246152962189 66 | pair_coeff * * 100.0 1.12246152962189 67 | 68 | ################################################################### 69 | 70 | ################################################################### 71 | # Pair interaction between bonded atoms 72 | 73 | bond_style harmonic 74 | bond_coeff 1 60.0 1.1 75 | 76 | ################################################### 77 | ### 78 | # Set up fixes 79 | ### 80 | variable seed equal 54541 81 | 82 | fix 1 all nve/asphere ###NVE ensemble 83 | fix 2 all langevin 1.0 1.0 0.5 ${seed} angmom 3.333 ###Langevin integrator Tstart Tstop 1/friction rndseed 84 | 85 | ################################################### 86 | ### 87 | # Output thermo data to a file 88 | ### 89 | variable t equal step 90 | variable cbtemp equal temp 91 | variable cbepair equal epair 92 | variable cbemol equal emol 93 | variable cbebond equal ebond 94 | variable cbeangle equal eangle 95 | 96 | fix ther all print 10000 "$t ${cbtemp} ${cbepair} ${cbemol}" file thermo.first_equilib screen no 97 | 98 | ##### Sample thermodynamic info (temperature, energy, pressure, etc.) ##### 99 | thermo 1000 100 | thermo_style custom step temp epair press vol 101 | ############################################################################ 102 | 103 | ### 104 | # set timestep of integrator 105 | ### 106 | timestep 0.01 107 | 108 | ### 109 | # run integration for a number of steps 110 | ### 111 | run 20000 112 | 113 | 114 | ### 115 | # Change the potentials to lj and FENE 116 | ### 117 | 118 | pair_style lj/cut 1.12246152962189 119 | pair_modify shift yes 120 | pair_coeff 1 1 1.0 1.0 1.12246152962189 121 | 122 | run 10000 123 | 124 | bond_style fene 125 | special_bonds fene #<=== I M P O R T A N T (new command) 126 | bond_coeff 1 30.0 1.6 1.0 1.0 127 | 128 | run 50000 129 | 130 | # now a long run to forget the initial configuration 131 | 132 | run 100000 133 | 134 | write_restart restart.1stequilib 135 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/in.twistDNA_2ndequilib: -------------------------------------------------------------------------------- 1 | 2 | ### 3 | # Box and units (use LJ units and periodic boundaries) 4 | ### 5 | 6 | units lj 7 | 8 | atom_style hybrid angle ellipsoid 9 | 10 | boundary p p p 11 | 12 | ### 13 | # Pair interactions require lists of neighbours to be calculated 14 | ### 15 | neighbor 1.9 bin 16 | neigh_modify every 1 delay 1 check yes 17 | 18 | 19 | ### READ "start" data file ### 20 | read_restart restart.1stequilib 21 | ###################### 22 | 23 | ###################### 24 | ### reset timestep ### 25 | reset_timestep 0 26 | ###################### 27 | 28 | ### 29 | # Define groups (atom type 1 is group 'all') 30 | ### 31 | group all type 1 32 | 33 | ### 34 | # Dump configs 35 | ### 36 | 37 | # A dump file with bead orientations 38 | compute quat all property/atom quatw quati quatj quatk 39 | dump d2 all custom 5000 dump_2ndequilib.DNA id type xs ys zs ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] 40 | 41 | ################################################################### 42 | # Stiffness term 43 | # 44 | # E = K * (1+cos(theta)), K>0 45 | # 46 | angle_style hybrid cosine polytorsion 47 | angle_coeff 1 cosine 40.0 48 | angle_coeff 2 polytorsion 70.0 30.0 49 | 50 | ################################################################### 51 | 52 | ################################################################### 53 | # Pair interaction between non-bonded atoms 54 | 55 | pair_style lj/cut 1.12246152962189 56 | pair_modify shift yes 57 | pair_coeff 1 1 1.0 1.0 1.12246152962189 58 | 59 | ################################################################### 60 | 61 | ################################################################### 62 | # Pair interaction between bonded atoms 63 | 64 | bond_style fene 65 | special_bonds fene #<=== I M P O R T A N T (new command) 66 | bond_coeff 1 30.0 1.6 1.0 1.0 67 | 68 | ################################################### 69 | ### 70 | # Set up fixes 71 | ### 72 | variable seed equal 54541 73 | 74 | fix 1 all nve/asphere ###NVE ensemble 75 | fix 2 all langevin 1.0 1.0 0.5 ${seed} angmom 3.333 ###Langevin integrator Tstart Tstop 1/friction rndseed 76 | 77 | ################################################### 78 | ### 79 | # Output thermo data to a file 80 | ### 81 | variable t equal step 82 | variable cbtemp equal temp 83 | variable cbepair equal epair 84 | variable cbemol equal emol 85 | variable cbebond equal ebond 86 | variable cbeangle equal eangle 87 | 88 | fix ther all print 10000 "$t ${cbtemp} ${cbepair} ${cbemol}" file thermo_2ndequilib.dat screen no 89 | 90 | ##### Sample thermodynamic info (temperature, energy, pressure, etc.) ##### 91 | thermo 1000 92 | thermo_style custom step temp epair vol 93 | ############################################################################ 94 | 95 | ### 96 | # set timestep of integrator 97 | ### 98 | timestep 0.01 99 | 100 | ### 101 | # run integration for a number of steps 102 | ### 103 | 104 | run 100000 105 | 106 | write_restart restart.2ndequilib 107 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/lammps.input: -------------------------------------------------------------------------------- 1 | LAMMPS data file 2 | 3 | 100 atoms 4 | 100 ellipsoids 5 | 100 bonds 6 | 200 angles 7 | 8 | 1 atom types 9 | 1 bond types 10 | 2 angle types 11 | 12 | -30 30 xlo xhi 13 | -30 30 ylo yhi 14 | -30 30 zlo zhi 15 | 16 | 17 | Masses 18 | 19 | 1 1 20 | 21 | Atoms 22 | 23 | 1 1 -7.5 -7.5 0 1 1 1.90986 24 | 2 1 -7.5 -6 0 1 1 1.90986 25 | 3 1 -7.5 -4.5 0 1 1 1.90986 26 | 4 1 -7.5 -3 0 1 1 1.90986 27 | 5 1 -7.5 -1.5 0 1 1 1.90986 28 | 6 1 -7.5 0 0 1 1 1.90986 29 | 7 1 -7.5 1.5 0 1 1 1.90986 30 | 8 1 -7.5 3 0 1 1 1.90986 31 | 9 1 -7.5 4.5 0 1 1 1.90986 32 | 10 1 -7.5 6 0 1 1 1.90986 33 | 11 1 -6 6 0 1 1 1.90986 34 | 12 1 -6 4.5 0 1 1 1.90986 35 | 13 1 -6 3 0 1 1 1.90986 36 | 14 1 -6 1.5 0 1 1 1.90986 37 | 15 1 -6 0 0 1 1 1.90986 38 | 16 1 -6 -1.5 0 1 1 1.90986 39 | 17 1 -6 -3 0 1 1 1.90986 40 | 18 1 -6 -4.5 0 1 1 1.90986 41 | 19 1 -6 -6 0 1 1 1.90986 42 | 20 1 -4.5 -6 0 1 1 1.90986 43 | 21 1 -4.5 -4.5 0 1 1 1.90986 44 | 22 1 -4.5 -3 0 1 1 1.90986 45 | 23 1 -4.5 -1.5 0 1 1 1.90986 46 | 24 1 -4.5 0 0 1 1 1.90986 47 | 25 1 -4.5 1.5 0 1 1 1.90986 48 | 26 1 -4.5 3 0 1 1 1.90986 49 | 27 1 -4.5 4.5 0 1 1 1.90986 50 | 28 1 -4.5 6 0 1 1 1.90986 51 | 29 1 -3 6 0 1 1 1.90986 52 | 30 1 -3 4.5 0 1 1 1.90986 53 | 31 1 -3 3 0 1 1 1.90986 54 | 32 1 -3 1.5 0 1 1 1.90986 55 | 33 1 -3 0 0 1 1 1.90986 56 | 34 1 -3 -1.5 0 1 1 1.90986 57 | 35 1 -3 -3 0 1 1 1.90986 58 | 36 1 -3 -4.5 0 1 1 1.90986 59 | 37 1 -3 -6 0 1 1 1.90986 60 | 38 1 -1.5 -6 0 1 1 1.90986 61 | 39 1 -1.5 -4.5 0 1 1 1.90986 62 | 40 1 -1.5 -3 0 1 1 1.90986 63 | 41 1 -1.5 -1.5 0 1 1 1.90986 64 | 42 1 -1.5 0 0 1 1 1.90986 65 | 43 1 -1.5 1.5 0 1 1 1.90986 66 | 44 1 -1.5 3 0 1 1 1.90986 67 | 45 1 -1.5 4.5 0 1 1 1.90986 68 | 46 1 -1.5 6 0 1 1 1.90986 69 | 47 1 0 6 0 1 1 1.90986 70 | 48 1 0 4.5 0 1 1 1.90986 71 | 49 1 0 3 0 1 1 1.90986 72 | 50 1 0 1.5 0 1 1 1.90986 73 | 51 1 0 0 0 1 1 1.90986 74 | 52 1 0 -1.5 0 1 1 1.90986 75 | 53 1 0 -3 0 1 1 1.90986 76 | 54 1 0 -4.5 0 1 1 1.90986 77 | 55 1 0 -6 0 1 1 1.90986 78 | 56 1 1.5 -6 0 1 1 1.90986 79 | 57 1 1.5 -4.5 0 1 1 1.90986 80 | 58 1 1.5 -3 0 1 1 1.90986 81 | 59 1 1.5 -1.5 0 1 1 1.90986 82 | 60 1 1.5 0 0 1 1 1.90986 83 | 61 1 1.5 1.5 0 1 1 1.90986 84 | 62 1 1.5 3 0 1 1 1.90986 85 | 63 1 1.5 4.5 0 1 1 1.90986 86 | 64 1 1.5 6 0 1 1 1.90986 87 | 65 1 3 6 0 1 1 1.90986 88 | 66 1 3 4.5 0 1 1 1.90986 89 | 67 1 3 3 0 1 1 1.90986 90 | 68 1 3 1.5 0 1 1 1.90986 91 | 69 1 3 0 0 1 1 1.90986 92 | 70 1 3 -1.5 0 1 1 1.90986 93 | 71 1 3 -3 0 1 1 1.90986 94 | 72 1 3 -4.5 0 1 1 1.90986 95 | 73 1 3 -6 0 1 1 1.90986 96 | 74 1 4.5 -6 0 1 1 1.90986 97 | 75 1 4.5 -4.5 0 1 1 1.90986 98 | 76 1 4.5 -3 0 1 1 1.90986 99 | 77 1 4.5 -1.5 0 1 1 1.90986 100 | 78 1 4.5 0 0 1 1 1.90986 101 | 79 1 4.5 1.5 0 1 1 1.90986 102 | 80 1 4.5 3 0 1 1 1.90986 103 | 81 1 4.5 4.5 0 1 1 1.90986 104 | 82 1 4.5 6 0 1 1 1.90986 105 | 83 1 6 6 0 1 1 1.90986 106 | 84 1 6 4.5 0 1 1 1.90986 107 | 85 1 6 3 0 1 1 1.90986 108 | 86 1 6 1.5 0 1 1 1.90986 109 | 87 1 6 0 0 1 1 1.90986 110 | 88 1 6 -1.5 0 1 1 1.90986 111 | 89 1 6 -3 0 1 1 1.90986 112 | 90 1 6 -4.5 0 1 1 1.90986 113 | 91 1 6 -6 0 1 1 1.90986 114 | 92 1 6 -7.5 0 1 1 1.90986 115 | 93 1 4.5 -7.5 0 1 1 1.90986 116 | 94 1 3 -7.5 0 1 1 1.90986 117 | 95 1 1.5 -7.5 0 1 1 1.90986 118 | 96 1 0 -7.5 0 1 1 1.90986 119 | 97 1 -1.5 -7.5 0 1 1 1.90986 120 | 98 1 -3 -7.5 0 1 1 1.90986 121 | 99 1 -4.5 -7.5 0 1 1 1.90986 122 | 100 1 -6 -7.5 0 1 1 1.90986 123 | 124 | Ellipsoids 125 | 126 | 1 1 1 1 0.707107 -0.707107 0 0 127 | 2 1 1 1 0.707107 -0.707107 0 0 128 | 3 1 1 1 0.707107 -0.707107 0 0 129 | 4 1 1 1 0.707107 -0.707107 0 0 130 | 5 1 1 1 0.707107 -0.707107 0 0 131 | 6 1 1 1 0.707107 -0.707107 0 0 132 | 7 1 1 1 0.707107 -0.707107 0 0 133 | 8 1 1 1 0.707107 -0.707107 0 0 134 | 9 1 1 1 0.707107 -0.707107 0 0 135 | 10 1 1 1 0.5 -0.5 0.5 -0.5 136 | 11 1 1 1 0 0 0.707107 -0.707107 137 | 12 1 1 1 0 0 0.707107 -0.707107 138 | 13 1 1 1 0 0 0.707107 -0.707107 139 | 14 1 1 1 0 0 0.707107 -0.707107 140 | 15 1 1 1 0 0 0.707107 -0.707107 141 | 16 1 1 1 0 0 0.707107 -0.707107 142 | 17 1 1 1 0 0 0.707107 -0.707107 143 | 18 1 1 1 0 0 0.707107 -0.707107 144 | 19 1 1 1 0.5 -0.5 0.5 -0.5 145 | 20 1 1 1 0.707107 -0.707107 0 0 146 | 21 1 1 1 0.707107 -0.707107 0 0 147 | 22 1 1 1 0.707107 -0.707107 0 0 148 | 23 1 1 1 0.707107 -0.707107 0 0 149 | 24 1 1 1 0.707107 -0.707107 0 0 150 | 25 1 1 1 0.707107 -0.707107 0 0 151 | 26 1 1 1 0.707107 -0.707107 0 0 152 | 27 1 1 1 0.707107 -0.707107 0 0 153 | 28 1 1 1 0.5 -0.5 0.5 -0.5 154 | 29 1 1 1 0 0 0.707107 -0.707107 155 | 30 1 1 1 0 0 0.707107 -0.707107 156 | 31 1 1 1 0 0 0.707107 -0.707107 157 | 32 1 1 1 0 0 0.707107 -0.707107 158 | 33 1 1 1 0 0 0.707107 -0.707107 159 | 34 1 1 1 0 0 0.707107 -0.707107 160 | 35 1 1 1 0 0 0.707107 -0.707107 161 | 36 1 1 1 0 0 0.707107 -0.707107 162 | 37 1 1 1 0.5 -0.5 0.5 -0.5 163 | 38 1 1 1 0.707107 -0.707107 0 0 164 | 39 1 1 1 0.707107 -0.707107 0 0 165 | 40 1 1 1 0.707107 -0.707107 0 0 166 | 41 1 1 1 0.707107 -0.707107 0 0 167 | 42 1 1 1 0.707107 -0.707107 0 0 168 | 43 1 1 1 0.707107 -0.707107 0 0 169 | 44 1 1 1 0.707107 -0.707107 0 0 170 | 45 1 1 1 0.707107 -0.707107 0 0 171 | 46 1 1 1 0.5 -0.5 0.5 -0.5 172 | 47 1 1 1 0 0 0.707107 -0.707107 173 | 48 1 1 1 0 0 0.707107 -0.707107 174 | 49 1 1 1 0 0 0.707107 -0.707107 175 | 50 1 1 1 0 0 0.707107 -0.707107 176 | 51 1 1 1 0 0 0.707107 -0.707107 177 | 52 1 1 1 0 0 0.707107 -0.707107 178 | 53 1 1 1 0 0 0.707107 -0.707107 179 | 54 1 1 1 0 0 0.707107 -0.707107 180 | 55 1 1 1 0.5 -0.5 0.5 -0.5 181 | 56 1 1 1 0.707107 -0.707107 0 0 182 | 57 1 1 1 0.707107 -0.707107 0 0 183 | 58 1 1 1 0.707107 -0.707107 0 0 184 | 59 1 1 1 0.707107 -0.707107 0 0 185 | 60 1 1 1 0.707107 -0.707107 0 0 186 | 61 1 1 1 0.707107 -0.707107 0 0 187 | 62 1 1 1 0.707107 -0.707107 0 0 188 | 63 1 1 1 0.707107 -0.707107 0 0 189 | 64 1 1 1 0.5 -0.5 0.5 -0.5 190 | 65 1 1 1 0 0 0.707107 -0.707107 191 | 66 1 1 1 0 0 0.707107 -0.707107 192 | 67 1 1 1 0 0 0.707107 -0.707107 193 | 68 1 1 1 0 0 0.707107 -0.707107 194 | 69 1 1 1 0 0 0.707107 -0.707107 195 | 70 1 1 1 0 0 0.707107 -0.707107 196 | 71 1 1 1 0 0 0.707107 -0.707107 197 | 72 1 1 1 0 0 0.707107 -0.707107 198 | 73 1 1 1 0.5 -0.5 0.5 -0.5 199 | 74 1 1 1 0.707107 -0.707107 0 0 200 | 75 1 1 1 0.707107 -0.707107 0 0 201 | 76 1 1 1 0.707107 -0.707107 0 0 202 | 77 1 1 1 0.707107 -0.707107 0 0 203 | 78 1 1 1 0.707107 -0.707107 0 0 204 | 79 1 1 1 0.707107 -0.707107 0 0 205 | 80 1 1 1 0.707107 -0.707107 0 0 206 | 81 1 1 1 0.707107 -0.707107 0 0 207 | 82 1 1 1 0.5 -0.5 0.5 -0.5 208 | 83 1 1 1 0 0 0.707107 -0.707107 209 | 84 1 1 1 0 0 0.707107 -0.707107 210 | 85 1 1 1 0 0 0.707107 -0.707107 211 | 86 1 1 1 0 0 0.707107 -0.707107 212 | 87 1 1 1 0 0 0.707107 -0.707107 213 | 88 1 1 1 0 0 0.707107 -0.707107 214 | 89 1 1 1 0 0 0.707107 -0.707107 215 | 90 1 1 1 0 0 0.707107 -0.707107 216 | 91 1 1 1 0 0 0.707107 -0.707107 217 | 92 1 1 1 0.5 -0.5 -0.5 0.5 218 | 93 1 1 1 0.5 -0.5 -0.5 0.5 219 | 94 1 1 1 0.5 -0.5 -0.5 0.5 220 | 95 1 1 1 0.5 -0.5 -0.5 0.5 221 | 96 1 1 1 0.5 -0.5 -0.5 0.5 222 | 97 1 1 1 0.5 -0.5 -0.5 0.5 223 | 98 1 1 1 0.5 -0.5 -0.5 0.5 224 | 99 1 1 1 0.5 -0.5 -0.5 0.5 225 | 100 1 1 1 0.5 -0.5 -0.5 0.5 226 | 227 | Velocities 228 | 229 | 1 0 0 0 0 0 0 230 | 2 0 0 0 0 0 0 231 | 3 0 0 0 0 0 0 232 | 4 0 0 0 0 0 0 233 | 5 0 0 0 0 0 0 234 | 6 0 0 0 0 0 0 235 | 7 0 0 0 0 0 0 236 | 8 0 0 0 0 0 0 237 | 9 0 0 0 0 0 0 238 | 10 0 0 0 0 0 0 239 | 11 0 0 0 0 0 0 240 | 12 0 0 0 0 0 0 241 | 13 0 0 0 0 0 0 242 | 14 0 0 0 0 0 0 243 | 15 0 0 0 0 0 0 244 | 16 0 0 0 0 0 0 245 | 17 0 0 0 0 0 0 246 | 18 0 0 0 0 0 0 247 | 19 0 0 0 0 0 0 248 | 20 0 0 0 0 0 0 249 | 21 0 0 0 0 0 0 250 | 22 0 0 0 0 0 0 251 | 23 0 0 0 0 0 0 252 | 24 0 0 0 0 0 0 253 | 25 0 0 0 0 0 0 254 | 26 0 0 0 0 0 0 255 | 27 0 0 0 0 0 0 256 | 28 0 0 0 0 0 0 257 | 29 0 0 0 0 0 0 258 | 30 0 0 0 0 0 0 259 | 31 0 0 0 0 0 0 260 | 32 0 0 0 0 0 0 261 | 33 0 0 0 0 0 0 262 | 34 0 0 0 0 0 0 263 | 35 0 0 0 0 0 0 264 | 36 0 0 0 0 0 0 265 | 37 0 0 0 0 0 0 266 | 38 0 0 0 0 0 0 267 | 39 0 0 0 0 0 0 268 | 40 0 0 0 0 0 0 269 | 41 0 0 0 0 0 0 270 | 42 0 0 0 0 0 0 271 | 43 0 0 0 0 0 0 272 | 44 0 0 0 0 0 0 273 | 45 0 0 0 0 0 0 274 | 46 0 0 0 0 0 0 275 | 47 0 0 0 0 0 0 276 | 48 0 0 0 0 0 0 277 | 49 0 0 0 0 0 0 278 | 50 0 0 0 0 0 0 279 | 51 0 0 0 0 0 0 280 | 52 0 0 0 0 0 0 281 | 53 0 0 0 0 0 0 282 | 54 0 0 0 0 0 0 283 | 55 0 0 0 0 0 0 284 | 56 0 0 0 0 0 0 285 | 57 0 0 0 0 0 0 286 | 58 0 0 0 0 0 0 287 | 59 0 0 0 0 0 0 288 | 60 0 0 0 0 0 0 289 | 61 0 0 0 0 0 0 290 | 62 0 0 0 0 0 0 291 | 63 0 0 0 0 0 0 292 | 64 0 0 0 0 0 0 293 | 65 0 0 0 0 0 0 294 | 66 0 0 0 0 0 0 295 | 67 0 0 0 0 0 0 296 | 68 0 0 0 0 0 0 297 | 69 0 0 0 0 0 0 298 | 70 0 0 0 0 0 0 299 | 71 0 0 0 0 0 0 300 | 72 0 0 0 0 0 0 301 | 73 0 0 0 0 0 0 302 | 74 0 0 0 0 0 0 303 | 75 0 0 0 0 0 0 304 | 76 0 0 0 0 0 0 305 | 77 0 0 0 0 0 0 306 | 78 0 0 0 0 0 0 307 | 79 0 0 0 0 0 0 308 | 80 0 0 0 0 0 0 309 | 81 0 0 0 0 0 0 310 | 82 0 0 0 0 0 0 311 | 83 0 0 0 0 0 0 312 | 84 0 0 0 0 0 0 313 | 85 0 0 0 0 0 0 314 | 86 0 0 0 0 0 0 315 | 87 0 0 0 0 0 0 316 | 88 0 0 0 0 0 0 317 | 89 0 0 0 0 0 0 318 | 90 0 0 0 0 0 0 319 | 91 0 0 0 0 0 0 320 | 92 0 0 0 0 0 0 321 | 93 0 0 0 0 0 0 322 | 94 0 0 0 0 0 0 323 | 95 0 0 0 0 0 0 324 | 96 0 0 0 0 0 0 325 | 97 0 0 0 0 0 0 326 | 98 0 0 0 0 0 0 327 | 99 0 0 0 0 0 0 328 | 100 0 0 0 0 0 0 329 | 330 | Bonds 331 | 332 | 1 1 1 2 333 | 2 1 2 3 334 | 3 1 3 4 335 | 4 1 4 5 336 | 5 1 5 6 337 | 6 1 6 7 338 | 7 1 7 8 339 | 8 1 8 9 340 | 9 1 9 10 341 | 10 1 10 11 342 | 11 1 11 12 343 | 12 1 12 13 344 | 13 1 13 14 345 | 14 1 14 15 346 | 15 1 15 16 347 | 16 1 16 17 348 | 17 1 17 18 349 | 18 1 18 19 350 | 19 1 19 20 351 | 20 1 20 21 352 | 21 1 21 22 353 | 22 1 22 23 354 | 23 1 23 24 355 | 24 1 24 25 356 | 25 1 25 26 357 | 26 1 26 27 358 | 27 1 27 28 359 | 28 1 28 29 360 | 29 1 29 30 361 | 30 1 30 31 362 | 31 1 31 32 363 | 32 1 32 33 364 | 33 1 33 34 365 | 34 1 34 35 366 | 35 1 35 36 367 | 36 1 36 37 368 | 37 1 37 38 369 | 38 1 38 39 370 | 39 1 39 40 371 | 40 1 40 41 372 | 41 1 41 42 373 | 42 1 42 43 374 | 43 1 43 44 375 | 44 1 44 45 376 | 45 1 45 46 377 | 46 1 46 47 378 | 47 1 47 48 379 | 48 1 48 49 380 | 49 1 49 50 381 | 50 1 50 51 382 | 51 1 51 52 383 | 52 1 52 53 384 | 53 1 53 54 385 | 54 1 54 55 386 | 55 1 55 56 387 | 56 1 56 57 388 | 57 1 57 58 389 | 58 1 58 59 390 | 59 1 59 60 391 | 60 1 60 61 392 | 61 1 61 62 393 | 62 1 62 63 394 | 63 1 63 64 395 | 64 1 64 65 396 | 65 1 65 66 397 | 66 1 66 67 398 | 67 1 67 68 399 | 68 1 68 69 400 | 69 1 69 70 401 | 70 1 70 71 402 | 71 1 71 72 403 | 72 1 72 73 404 | 73 1 73 74 405 | 74 1 74 75 406 | 75 1 75 76 407 | 76 1 76 77 408 | 77 1 77 78 409 | 78 1 78 79 410 | 79 1 79 80 411 | 80 1 80 81 412 | 81 1 81 82 413 | 82 1 82 83 414 | 83 1 83 84 415 | 84 1 84 85 416 | 85 1 85 86 417 | 86 1 86 87 418 | 87 1 87 88 419 | 88 1 88 89 420 | 89 1 89 90 421 | 90 1 90 91 422 | 91 1 91 92 423 | 92 1 92 93 424 | 93 1 93 94 425 | 94 1 94 95 426 | 95 1 95 96 427 | 96 1 96 97 428 | 97 1 97 98 429 | 98 1 98 99 430 | 99 1 99 100 431 | 100 1 100 1 432 | 433 | Angles 434 | 435 | 1 2 1 2 2 436 | 2 1 1 2 3 437 | 3 2 2 3 3 438 | 4 1 2 3 4 439 | 5 2 3 4 4 440 | 6 1 3 4 5 441 | 7 2 4 5 5 442 | 8 1 4 5 6 443 | 9 2 5 6 6 444 | 10 1 5 6 7 445 | 11 2 6 7 7 446 | 12 1 6 7 8 447 | 13 2 7 8 8 448 | 14 1 7 8 9 449 | 15 2 8 9 9 450 | 16 1 8 9 10 451 | 17 2 9 10 10 452 | 18 1 9 10 11 453 | 19 2 10 11 11 454 | 20 1 10 11 12 455 | 21 2 11 12 12 456 | 22 1 11 12 13 457 | 23 2 12 13 13 458 | 24 1 12 13 14 459 | 25 2 13 14 14 460 | 26 1 13 14 15 461 | 27 2 14 15 15 462 | 28 1 14 15 16 463 | 29 2 15 16 16 464 | 30 1 15 16 17 465 | 31 2 16 17 17 466 | 32 1 16 17 18 467 | 33 2 17 18 18 468 | 34 1 17 18 19 469 | 35 2 18 19 19 470 | 36 1 18 19 20 471 | 37 2 19 20 20 472 | 38 1 19 20 21 473 | 39 2 20 21 21 474 | 40 1 20 21 22 475 | 41 2 21 22 22 476 | 42 1 21 22 23 477 | 43 2 22 23 23 478 | 44 1 22 23 24 479 | 45 2 23 24 24 480 | 46 1 23 24 25 481 | 47 2 24 25 25 482 | 48 1 24 25 26 483 | 49 2 25 26 26 484 | 50 1 25 26 27 485 | 51 2 26 27 27 486 | 52 1 26 27 28 487 | 53 2 27 28 28 488 | 54 1 27 28 29 489 | 55 2 28 29 29 490 | 56 1 28 29 30 491 | 57 2 29 30 30 492 | 58 1 29 30 31 493 | 59 2 30 31 31 494 | 60 1 30 31 32 495 | 61 2 31 32 32 496 | 62 1 31 32 33 497 | 63 2 32 33 33 498 | 64 1 32 33 34 499 | 65 2 33 34 34 500 | 66 1 33 34 35 501 | 67 2 34 35 35 502 | 68 1 34 35 36 503 | 69 2 35 36 36 504 | 70 1 35 36 37 505 | 71 2 36 37 37 506 | 72 1 36 37 38 507 | 73 2 37 38 38 508 | 74 1 37 38 39 509 | 75 2 38 39 39 510 | 76 1 38 39 40 511 | 77 2 39 40 40 512 | 78 1 39 40 41 513 | 79 2 40 41 41 514 | 80 1 40 41 42 515 | 81 2 41 42 42 516 | 82 1 41 42 43 517 | 83 2 42 43 43 518 | 84 1 42 43 44 519 | 85 2 43 44 44 520 | 86 1 43 44 45 521 | 87 2 44 45 45 522 | 88 1 44 45 46 523 | 89 2 45 46 46 524 | 90 1 45 46 47 525 | 91 2 46 47 47 526 | 92 1 46 47 48 527 | 93 2 47 48 48 528 | 94 1 47 48 49 529 | 95 2 48 49 49 530 | 96 1 48 49 50 531 | 97 2 49 50 50 532 | 98 1 49 50 51 533 | 99 2 50 51 51 534 | 100 1 50 51 52 535 | 101 2 51 52 52 536 | 102 1 51 52 53 537 | 103 2 52 53 53 538 | 104 1 52 53 54 539 | 105 2 53 54 54 540 | 106 1 53 54 55 541 | 107 2 54 55 55 542 | 108 1 54 55 56 543 | 109 2 55 56 56 544 | 110 1 55 56 57 545 | 111 2 56 57 57 546 | 112 1 56 57 58 547 | 113 2 57 58 58 548 | 114 1 57 58 59 549 | 115 2 58 59 59 550 | 116 1 58 59 60 551 | 117 2 59 60 60 552 | 118 1 59 60 61 553 | 119 2 60 61 61 554 | 120 1 60 61 62 555 | 121 2 61 62 62 556 | 122 1 61 62 63 557 | 123 2 62 63 63 558 | 124 1 62 63 64 559 | 125 2 63 64 64 560 | 126 1 63 64 65 561 | 127 2 64 65 65 562 | 128 1 64 65 66 563 | 129 2 65 66 66 564 | 130 1 65 66 67 565 | 131 2 66 67 67 566 | 132 1 66 67 68 567 | 133 2 67 68 68 568 | 134 1 67 68 69 569 | 135 2 68 69 69 570 | 136 1 68 69 70 571 | 137 2 69 70 70 572 | 138 1 69 70 71 573 | 139 2 70 71 71 574 | 140 1 70 71 72 575 | 141 2 71 72 72 576 | 142 1 71 72 73 577 | 143 2 72 73 73 578 | 144 1 72 73 74 579 | 145 2 73 74 74 580 | 146 1 73 74 75 581 | 147 2 74 75 75 582 | 148 1 74 75 76 583 | 149 2 75 76 76 584 | 150 1 75 76 77 585 | 151 2 76 77 77 586 | 152 1 76 77 78 587 | 153 2 77 78 78 588 | 154 1 77 78 79 589 | 155 2 78 79 79 590 | 156 1 78 79 80 591 | 157 2 79 80 80 592 | 158 1 79 80 81 593 | 159 2 80 81 81 594 | 160 1 80 81 82 595 | 161 2 81 82 82 596 | 162 1 81 82 83 597 | 163 2 82 83 83 598 | 164 1 82 83 84 599 | 165 2 83 84 84 600 | 166 1 83 84 85 601 | 167 2 84 85 85 602 | 168 1 84 85 86 603 | 169 2 85 86 86 604 | 170 1 85 86 87 605 | 171 2 86 87 87 606 | 172 1 86 87 88 607 | 173 2 87 88 88 608 | 174 1 87 88 89 609 | 175 2 88 89 89 610 | 176 1 88 89 90 611 | 177 2 89 90 90 612 | 178 1 89 90 91 613 | 179 2 90 91 91 614 | 180 1 90 91 92 615 | 181 2 91 92 92 616 | 182 1 91 92 93 617 | 183 2 92 93 93 618 | 184 1 92 93 94 619 | 185 2 93 94 94 620 | 186 1 93 94 95 621 | 187 2 94 95 95 622 | 188 1 94 95 96 623 | 189 2 95 96 96 624 | 190 1 95 96 97 625 | 191 2 96 97 97 626 | 192 1 96 97 98 627 | 193 2 97 98 98 628 | 194 1 97 98 99 629 | 195 2 98 99 99 630 | 196 1 98 99 100 631 | 197 2 99 100 100 632 | 198 1 99 100 1 633 | 199 1 100 1 2 634 | 200 2 100 1 1 635 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/lammps_restart2data_with_ellipsoids.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | path2lammps="~/work/lmp-7Dec15_openmpi_SL7" 4 | 5 | # In the current version of LAMMPS, the write_data command does not 6 | # output the ellipsoids 7 | 8 | if [[ ! $# == 2 ]]; then 9 | echo "Usage : lammps_restart2data_with_ellipsoids.sh input.restart output.data" 10 | exit 1 11 | fi 12 | 13 | infile=$1 14 | outfile=$2 15 | 16 | if [[ ! -f $infile ]];then 17 | echo "ERROR : Cannot find file $infile" 18 | exit 1 19 | fi 20 | 21 | if [[ -f $outfile ]]; then 22 | echo "ERROR : File $outfile already exists" 23 | exit 1 24 | fi 25 | 26 | ##### 27 | ##### 28 | 29 | ## Notes : 30 | # 1. LAMMPS complains that angle coeff must be set. 31 | # The script below assumes there are two angle 32 | # types - need to edit this if there are more. 33 | # Since no simulation is run, and coeff and not 34 | # output to the file, doesn't matter what these are. 35 | # 2. The script also assumes that all atoms are ellipsoids. 36 | # Not sure what would happen if we attempt to compute 37 | # quaternions for atoms which do not have that property. 38 | # 3. The compute shape seems to give the radius rather than 39 | # the diameter as stated in the LAMMPS manual. The data 40 | # file must specify radius. 41 | 42 | 43 | eval $path2lammps << EOF 44 | 45 | atom_style hybrid angle ellipsoid 46 | read_restart $infile 47 | 48 | angle_style cosine 49 | angle_coeff 1 20.0 50 | angle_coeff 2 20.0 51 | 52 | compute shap all property/atom shapex shapey shapez 53 | compute quat all property/atom quatw quati quatj quatk 54 | dump d2 all custom 1 temp_ell id c_shap[1] c_shap[2] c_shap[3] c_quat[1] c_quat[2] c_quat[3] c_quat[4] 55 | dump_modify d2 first yes 56 | run 0 57 | 58 | write_data temp_data nocoeff 59 | 60 | EOF 61 | 62 | 63 | ### Now count the number of ellipsoids in the data file 64 | Nell=$( awk 'BEGIN{A=0;V=0;}{ 65 | if ($1=="Velocities") {A=0;V=1;} 66 | if (A==1&&$1!="") {c+=$7} 67 | if ($1=="Atoms") {A=1;} 68 | }END{print c}' temp_data ) 69 | 70 | ### And make the output file 71 | awk -v c=$Nell '{ 72 | print; 73 | if ($2=="atoms") {print c " ellipsoids";} 74 | }' temp_data > $outfile 75 | 76 | echo "" >> $outfile 77 | echo " Ellipsoids" >> $outfile 78 | echo "" >> $outfile 79 | 80 | awk '{if (NR>9) print $1,$2*2,$3*2,$4*2,$5,$6,$7,$8}' temp_ell >> $outfile 81 | # radii are multipled by 2 82 | 83 | ## clean up 84 | rm temp_data temp_ell 85 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/linking_1stequilib.dat: -------------------------------------------------------------------------------- 1 | # step, Tw, Wr, Tw+Wr 2 | 0 0 -nan -nan 3 | 1000 -0.386421 0.43229 0.0458686 4 | 2000 -0.340809 0.506284 0.165475 5 | 3000 -0.950162 1.07585 0.125684 6 | 4000 -0.969409 1.05524 0.0858323 7 | 5000 -1.01085 1.02923 0.018376 8 | 6000 -0.944856 0.996356 0.0514999 9 | 7000 -0.795898 0.751211 -0.044687 10 | 8000 -0.51994 0.474876 -0.0450631 11 | 9000 -0.379568 0.455224 0.0756566 12 | 10000 -0.614269 0.663658 0.0493893 13 | 11000 -0.722672 0.608749 -0.113923 14 | 12000 -0.619276 0.604799 -0.0144776 15 | 13000 -0.407147 0.554943 0.147796 16 | 14000 -0.313015 0.288325 -0.02469 17 | 15000 -0.231974 0.370833 0.138859 18 | 16000 -0.209759 0.309006 0.0992463 19 | 17000 -0.400188 0.422016 0.0218282 20 | 18000 -0.398598 0.299259 -0.0993391 21 | 19000 -0.341051 0.36752 0.0264693 22 | 20000 0.11671 -0.0760742 0.040636 23 | 21000 0.0689918 -0.144011 -0.0750195 24 | 22000 0.275805 -0.193007 0.0827987 25 | 23000 0.220021 -0.230815 -0.0107945 26 | 24000 0.217666 -0.237012 -0.0193464 27 | 25000 0.0222507 -0.0675767 -0.045326 28 | 26000 0.159007 -0.212351 -0.0533442 29 | 27000 0.427002 -0.378387 0.0486145 30 | 28000 0.268187 -0.313861 -0.0456742 31 | 29000 0.430844 -0.325536 0.105308 32 | 30000 0.41194 -0.471332 -0.059392 33 | 31000 0.319564 -0.34529 -0.0257269 34 | 32000 0.426975 -0.361145 0.0658301 35 | 33000 0.307701 -0.30457 0.00313129 36 | 34000 0.269435 -0.224699 0.0447362 37 | 35000 0.0686663 -0.098766 -0.0300997 38 | 36000 0.0505074 -0.0274574 0.02305 39 | 37000 0.0356685 -0.108543 -0.0728746 40 | 38000 0.278734 -0.276027 0.00270714 41 | 39000 0.359909 -0.37922 -0.0193109 42 | 40000 0.236981 -0.241148 -0.00416658 43 | 41000 0.194018 -0.19658 -0.00256219 44 | 42000 0.0343545 0.0442661 0.0786206 45 | 43000 0.167983 -0.147862 0.0201204 46 | 44000 0.12674 -0.220942 -0.0942021 47 | 45000 0.381454 -0.416022 -0.0345683 48 | 46000 0.719937 -0.611803 0.108134 49 | 47000 0.495257 -0.545249 -0.0499914 50 | 48000 0.495982 -0.567335 -0.0713531 51 | 49000 0.499625 -0.526991 -0.0273656 52 | 50000 0.568425 -0.59067 -0.0222452 53 | 51000 0.63285 -0.603617 0.0292326 54 | 52000 0.469618 -0.553267 -0.0836497 55 | 53000 0.52895 -0.486261 0.0426887 56 | 54000 0.63495 -0.556772 0.078178 57 | 55000 0.66057 -0.560543 0.100027 58 | 56000 0.593259 -0.55121 0.0420482 59 | 57000 0.784295 -0.784081 0.000214301 60 | 58000 0.633929 -0.630184 0.00374426 61 | 59000 0.752566 -0.781594 -0.0290278 62 | 60000 0.572577 -0.602395 -0.0298176 63 | 61000 0.655854 -0.682514 -0.0266601 64 | 62000 0.70438 -0.67201 0.0323702 65 | 63000 0.5708 -0.617179 -0.0463794 66 | 64000 0.461833 -0.501712 -0.0398791 67 | 65000 0.365964 -0.421232 -0.0552672 68 | 66000 0.298141 -0.347063 -0.0489219 69 | 67000 0.182431 -0.143338 0.0390926 70 | 68000 -0.0769464 -0.0601983 -0.137145 71 | 69000 0.177316 -0.247968 -0.0706514 72 | 70000 0.102219 -0.185944 -0.0837245 73 | 71000 0.30911 -0.378365 -0.0692548 74 | 72000 0.491917 -0.41152 0.0803975 75 | 73000 0.396823 -0.379417 0.0174064 76 | 74000 0.175744 -0.238715 -0.0629706 77 | 75000 0.222827 -0.192667 0.0301598 78 | 76000 0.315411 -0.278951 0.0364606 79 | 77000 0.273616 -0.247766 0.0258497 80 | 78000 0.23127 -0.2213 0.00997043 81 | 79000 0.0865172 -0.136846 -0.0503289 82 | 80000 0.368478 -0.316017 0.0524608 83 | 81000 0.33233 -0.385399 -0.0530688 84 | 82000 0.276986 -0.366174 -0.0891879 85 | 83000 0.134203 -0.157236 -0.0230335 86 | 84000 0.333685 -0.31643 0.0172548 87 | 85000 0.235224 -0.223689 0.0115354 88 | 86000 0.171595 -0.148104 0.0234909 89 | 87000 0.201803 -0.123973 0.0778296 90 | 88000 0.36092 -0.317381 0.0435389 91 | 89000 0.10498 -0.184568 -0.0795879 92 | 90000 0.242726 -0.229893 0.0128329 93 | 91000 0.00213545 0.0583655 0.060501 94 | 92000 0.280742 -0.247889 0.0328528 95 | 93000 0.0607135 -0.120149 -0.0594354 96 | 94000 0.232804 -0.201895 0.0309091 97 | 95000 0.11591 -0.155272 -0.0393616 98 | 96000 0.160263 -0.25643 -0.096167 99 | 97000 0.21943 -0.291654 -0.0722234 100 | 98000 0.144363 -0.203262 -0.0588984 101 | 99000 0.220522 -0.229416 -0.0088933 102 | 100000 0.406497 -0.34994 0.0565574 103 | 101000 0.267387 -0.319918 -0.0525304 104 | 102000 0.235084 -0.37714 -0.142056 105 | 103000 0.036562 -0.156032 -0.11947 106 | 104000 -0.112354 0.12087 0.00851591 107 | 105000 0.0960553 -0.0892095 0.00684582 108 | 106000 0.121915 -0.1274 -0.00548488 109 | 107000 0.128724 -0.182157 -0.053433 110 | 108000 0.279491 -0.294484 -0.0149939 111 | 109000 0.0983092 -0.108484 -0.0101752 112 | 110000 0.187728 -0.171358 0.0163703 113 | 111000 0.3815 -0.364542 0.0169579 114 | 112000 0.0507223 -0.157168 -0.106446 115 | 113000 0.202994 -0.131628 0.0713667 116 | 114000 0.179872 -0.142128 0.0377433 117 | 115000 0.247659 -0.215592 0.0320668 118 | 116000 0.332467 -0.36016 -0.0276931 119 | 117000 0.279917 -0.290845 -0.0109277 120 | 118000 0.157238 -0.190428 -0.03319 121 | 119000 0.213844 -0.232129 -0.0182849 122 | 120000 -0.00348447 -0.0694999 -0.0729844 123 | 121000 0.0550992 -0.0906285 -0.0355294 124 | 122000 0.215104 -0.254598 -0.0394942 125 | 123000 0.0510389 0.0346442 0.0856831 126 | 124000 0.227823 -0.125438 0.102385 127 | 125000 0.143279 -0.192004 -0.0487257 128 | 126000 0.245401 -0.284217 -0.0388161 129 | 127000 0.216821 -0.240327 -0.023506 130 | 128000 0.238873 -0.220957 0.0179157 131 | 129000 0.348637 -0.314889 0.0337476 132 | 130000 0.241223 -0.285587 -0.044364 133 | 131000 0.347637 -0.359757 -0.0121198 134 | 132000 0.438613 -0.464594 -0.0259811 135 | 133000 0.532361 -0.597543 -0.0651815 136 | 134000 0.475118 -0.485859 -0.0107406 137 | 135000 0.518395 -0.501401 0.0169937 138 | 136000 0.452303 -0.508206 -0.0559032 139 | 137000 0.599397 -0.519765 0.0796328 140 | 138000 0.373113 -0.462273 -0.08916 141 | 139000 0.604753 -0.606677 -0.00192444 142 | 140000 0.45684 -0.567621 -0.110781 143 | 141000 0.755241 -0.746861 0.00838 144 | 142000 0.49739 -0.641661 -0.144271 145 | 143000 0.599298 -0.697353 -0.0980549 146 | 144000 0.652061 -0.683147 -0.0310856 147 | 145000 0.796702 -0.63264 0.164063 148 | 146000 0.705907 -0.70491 0.000996827 149 | 147000 0.509408 -0.577333 -0.0679252 150 | 148000 0.514684 -0.582138 -0.067454 151 | 149000 0.586882 -0.689292 -0.10241 152 | 150000 0.769776 -0.845506 -0.0757307 153 | 151000 0.728414 -0.795887 -0.0674733 154 | 152000 0.680684 -0.699417 -0.0187333 155 | 153000 0.628726 -0.676481 -0.0477551 156 | 154000 0.536385 -0.593203 -0.0568187 157 | 155000 0.735185 -0.729344 0.00584117 158 | 156000 0.737035 -0.830794 -0.0937592 159 | 157000 0.615258 -0.683002 -0.0677436 160 | 158000 0.67883 -0.761763 -0.0829336 161 | 159000 0.877485 -0.858611 0.018874 162 | 160000 0.8424 -0.912675 -0.0702747 163 | 161000 0.965008 -0.877859 0.087149 164 | 162000 0.519739 -0.529816 -0.0100766 165 | 163000 0.651445 -0.662686 -0.0112409 166 | 164000 0.648865 -0.605224 0.0436413 167 | 165000 0.857139 -0.893353 -0.0362141 168 | 166000 0.867579 -0.876909 -0.00932996 169 | 167000 0.740749 -0.853952 -0.113203 170 | 168000 0.996544 -1.00067 -0.00412989 171 | 169000 0.882681 -0.971374 -0.088693 172 | 170000 1.00913 -0.98787 0.0212562 173 | 171000 1.12236 -1.17605 -0.053685 174 | 172000 1.03616 -1.10385 -0.0676949 175 | 173000 1.16569 -1.15721 0.00847938 176 | 174000 0.948633 -0.816849 0.131784 177 | 175000 0.865203 -0.909489 -0.0442858 178 | 176000 0.73278 -0.889418 -0.156638 179 | 177000 0.949629 -0.956844 -0.00721532 180 | 178000 1.04871 -1.02666 0.0220427 181 | 179000 0.787617 -0.948839 -0.161222 182 | 180000 1.04404 -1.0272 0.0168348 183 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/measure_linking: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/tutorial6/setup/measure_linking -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/restart.1stequilib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/tutorial6/setup/restart.1stequilib -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/restart.2ndequilib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbrackley/simple_lammps_tutorial/d1c28bc57b00cdcd3517b489b5522c0dbe738e40/lammps_tutorial/tutorial6/setup/restart.2ndequilib -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/thermo.first_equilib: -------------------------------------------------------------------------------- 1 | # Fix print output for fix ther 2 | 10000 0.984585172232399 0 3.05950012557709 3 | 20000 0.977860510200023 0 3.18496723219369 4 | 30000 0.893920963588637 0 3.06417803822516 5 | 40000 1.0026131865024 0 22.6539734183562 6 | 50000 0.941270198953664 0 22.7474105765003 7 | 60000 0.84678905058619 0 22.8121853169229 8 | 70000 0.969473216223449 0 22.9374714303544 9 | 80000 1.11951286719786 0 22.6699963436238 10 | 90000 0.957491196136807 0 22.6165047837053 11 | 100000 1.06877735857859 0 22.5067600238178 12 | 110000 1.02907087355736 0 22.8934983955151 13 | 120000 0.934655926731069 0 22.4951846825503 14 | 130000 0.952413473799816 0 23.0929544133889 15 | 140000 0.837641606344569 0 22.8969510815333 16 | 150000 0.94682122599922 0 22.8124789481577 17 | 160000 1.27039212428966 0 22.8088409436039 18 | 170000 1.04257489189654 0 22.5758715100763 19 | 180000 0.841330759246792 0 22.7568193861859 20 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/setup/thermo_2ndequilib.dat: -------------------------------------------------------------------------------- 1 | # Fix print output for fix ther 2 | 10000 0.997656562357141 0 22.6869071659972 3 | 20000 0.835339666287333 0 23.2622811102316 4 | 30000 1.01453358470545 0 22.6263789692194 5 | 40000 1.14969033529649 0 22.7089215395373 6 | 50000 1.04275718817879 0 23.1264115411638 7 | 60000 1.03613244190181 0 22.7220329982732 8 | 70000 0.932381047115964 0 22.3400698725192 9 | 80000 1.11754598191917 0 22.7499243665438 10 | 90000 0.942165968161216 0 22.6516242084379 11 | 100000 0.878092484801325 0 22.6794413864216 12 | -------------------------------------------------------------------------------- /lammps_tutorial/tutorial6/supercoiled.lam: -------------------------------------------------------------------------------- 1 | ############################################### 2 | # LAMMPS script for a supercoiled loop 3 | ############################################### 4 | 5 | ### 6 | # Box and units (use LJ units and periodic boundaries) 7 | ### 8 | 9 | units lj # use lennard-jones (i.e. dimensionless) units 10 | atom_style hybrid angle ellipsoid # atoms with bonds, angles and orientations 11 | 12 | boundary p p p # all boundaries are periodic 13 | 14 | ### 15 | # Pair interactions require lists of neighbours to be calculated 16 | ### 17 | neighbor 1.9 bin 18 | neigh_modify every 1 delay 1 check yes 19 | 20 | 21 | ### 22 | # READ "start" data file 23 | ### 24 | read_data initial_configuration.txt 25 | 26 | ### 27 | # Reset timestep 28 | ### 29 | reset_timestep 0 30 | 31 | ### 32 | # Define groups 33 | ### 34 | group all type 1 35 | 36 | ### 37 | # Dump configurations 38 | ### 39 | compute quat all property/atom quatw quati quatj quatk 40 | dump d2 all custom 5000 dump.DNA id type xs ys zs ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] 41 | # compute the quaternion which describes the orientation of each bead 42 | # output along with coordinates 43 | 44 | 45 | ### 46 | # Set up interactions 47 | ### 48 | 49 | 50 | ################################################################### 51 | # Stiffness term 52 | # 53 | # E = K * (1+cos(theta)), K>0 54 | # 55 | angle_style hybrid cosine polytorsion 56 | angle_coeff 1 cosine 20.0 57 | angle_coeff 2 polytorsion 70.0 30.0 58 | 59 | ################################################################### 60 | 61 | ################################################################### 62 | # Pair interaction between non-bonded atoms 63 | 64 | pair_style lj/cut 1.12246152962189 65 | pair_modify shift yes 66 | pair_coeff 1 1 1.0 1.0 1.12246152962189 67 | 68 | ################################################################### 69 | 70 | ################################################################### 71 | # Pair interaction between bonded atoms 72 | 73 | bond_style fene 74 | special_bonds fene #<=== I M P O R T A N T (new command) 75 | bond_coeff 1 30.0 1.6 1.0 1.0 76 | 77 | 78 | ################################################### 79 | ### 80 | # Set up fixes 81 | ### 82 | variable seed equal 54541 83 | 84 | fix 1 all nve/asphere ###NVE ensemble 85 | fix 2 all langevin 1.0 1.0 0.5 ${seed} angmom 3.333 ###Langevin integrator Tstart Tstop 1/friction rndseed 86 | # the nve/asphere interates rotational motion as well as displacements 87 | # also need to add a command to the langevin fix to do the rotation 88 | 89 | ##### Output thermodynamic info (temperature, energy, pressure, etc.) ##### 90 | thermo 1000 91 | thermo_style custom step temp epair emol press vol 92 | ############################################################################ 93 | 94 | 95 | ##### Output thermodynamic info to file ################################### 96 | variable t equal step 97 | variable mytemp equal temp 98 | variable myepair equal epair 99 | fix mythermofile all print 1000 "$t ${mytemp} ${myepair}" file thermo_output.dat screen no 100 | ############################################################################ 101 | 102 | 103 | ### 104 | # set timestep of integrator 105 | ### 106 | timestep 0.01 107 | 108 | ## do run 109 | run 100000 110 | 111 | 112 | #### write a final restart file 113 | write_restart final.restart -------------------------------------------------------------------------------- /lammps_tutorial/vmdrc: -------------------------------------------------------------------------------- 1 | # first load all defaults 2 | play /usr/local/lib/vmd/.vmdrc 3 | 4 | ########################### 5 | # display settings 6 | 7 | # switch off the way far away things appear faint : 8 | display depthcue off 9 | # switch off the way far away things are smaller than close things : 10 | display projection Orthographic 11 | # switch off axes : 12 | axes location off 13 | # bg colour : 14 | color Display Background white 15 | 16 | 17 | ########################### 18 | # change the default VDW radii 19 | # function to apply the radii on loading a structure 20 | proc my_set_def_vdw {args} { 21 | lassign $args fname molid 22 | set my_sel [atomselect $molid all] 23 | $my_sel set radius 0.5 24 | $my_sel delete 25 | molinfo 0 set center "{0.0 0.0 0.0}" 26 | } 27 | # hook up the function. 28 | trace variable vmd_initialize_structure(0) w my_set_def_vdw 29 | trace variable vmd_initialize_structure(1) w my_set_def_vdw 30 | trace variable vmd_initialize_structure(2) w my_set_def_vdw 31 | trace variable vmd_initialize_structure(3) w my_set_def_vdw 32 | trace variable vmd_initialize_structure(4) w my_set_def_vdw 33 | trace variable vmd_initialize_structure(5) w my_set_def_vdw 34 | trace variable vmd_initialize_structure(6) w my_set_def_vdw 35 | 36 | # set default display style 37 | mol default style VDW 38 | --------------------------------------------------------------------------------