Calculation of the glass transition temperature of an amorphous system
Overview
- Build the atomistic system (e.g. PolymerModeler)
- Run LAMMPS: cool the system and shrink the box
- Analyze the output from LAMMPS: extract density vs. T
(Image courtesy Lorena Alzate)
Service proposal
- GET info on available services returns JSON
{
"polybuild": {
"input": {
"values": {
"monomer": {
"type": "string",
"desc": "Name of the basic repeating unit",
"values": ["pmma", "pe", "ps"]
},
"chains": {
"type": "integer",
"desc": "Number of chains to build"
},
"monomers": {
"type": "integer",
"desc": "Number of monomers in each chain (polydispersity)"
},
"interactions": {
"type": "string",
"desc": "Name of interactions between particles",
"values": ["LJ"]
},
"range": {
"type": "real",
"units": "Angstroms",
"desc": "Interaction range between particles"
},
"density": {
"type": "real",
"units": "g/cc",
"desc": "Density of the constructed amorphous system"
},
"temperature": {
"type": "real",
"units": "K",
"desc": "Temperature of the system while building"
},
"configurations": {
"type": "integer",
"desc": "Number of configurations per torsion during MC sampling",
},
"rotate_torsions": {
"type": "string",
"desc": "Specify how many torsions in each monomer are rotated",
"values": ["all", "only_between"]
},
"torsion_probs": {
"type": "string",
"desc": "Specify how torsion angles are assigned",
"values": ["random", "fixed", "sp2", "sp3"]
},
"forcefield": {
"type": "string",
"desc": "Name of the forcefield to apply for LAMMPS data file",
"values": ["Dreiding"]
}
}
},
"output": {
"files": ["lammps_data_file"]
}
},
"lammps": {
"input": {
"files": ["lammps_script", "lammps_data_file"]
},
"output": {
"files": ["lammps_log_file"]
},
"submit_options": {
"cores": {
"type": "integer",
"desc": "Number of cores on which to run LAMMPS"
},
"walltime": {
"type": "real",
"units": "hours",
"desc": "Requested simulation time for LAMMPS"
}
}
}
"Tg": {
"script": "calcTg.py",
"input": {
"files": ["lammps_log_file"]
},
"output": {
"values": {
"Tg": {
"type": "real",
"units": "K",
"desc": "Glass transition temperature"
}
"density": {
"type": "array",
"units": "g/cc",
"desc": "System density over MD steps"
},
"temperature": {
"type": "array",
"units": "K",
"desc": "System temperature over MD steps"
}
}
}
}
}
- Construct JSON input describing a workflow
- polybuild: build the atomistic system
- lammps: run LAMMPS to cool and compress
- Tg: identify Tg from LAMMPS thermo output
{
"tasks": ["polybuild", "lammps", "Tg"],
"polybuild": {
"input": {
"values": {
"monomer": "pmma",
"chains": 10,
"monomers": 5,
"interactions": "LJ",
"range": 6.0,
"density": 0.5,
"temperature": 300,
"configurations": 50,
"rotate_torsions": "all",
"torsion_probs": "random"
"forcefield": "Dreiding"
}
},
"output": {
"files": {
"lammps_data_file": "polymer.data"
}
}
},
"lammps": {
"input": {
"files": {
"lammps_script": {
"contents": "units real\natom_style full\nboundary p p p\nspecial_bonds lj/coul 0.0 0.0 1.0 dihedral yes\ndielectric 1.0\npair_style lj/cut 6.0\nbond_style harmonic\nangle_style harmonic\ndihedral_style harmonic\nimproper_style harmonic\nread_data polymer.data\nneighbor 2.0 bin\nthermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press pxx pyy pzz pxy pxz pyz lx ly lz\nthermo 50\nthermo_modify flush yes\nMINIMIZE\ndump 1 all custom 1 polymer.dump id mol type xu yu zu\ndump_modify 1 format \"%d %d %d %.10f %.10f %.10f\"\nrun 0\nundump 1\nwrite_restart polymer.restart\n"
}
"lammps_data_file": "polymer.data"
}
},
"output": {
"files": {
"lammps_log_file": "log.lammps"
}
},
"submit_options": {
"cores": 4,
"walltime": 12.0
}
}
}