lammps中的atom_style(原子类型)的选择

atom_style定义了模拟过程中应选择什么系列的原子。

原子类型考虑的效应简述
anglebonds and anglesbead-spring polymers with stiffness
atomiconly the default values粗颗粒液体,固体,金属
bodymass, inertia moments, quaternion, angular momentumarbitrary bodies
bondbondsbead-spring polymers
chargechargeatomic system with charges
dielectricdipole, area, curvaturesystem with surface polarization
dipolecharge and dipole momentsystem with dipolar particles
dpdinternal temperature and internal energiesDPD particles
edpdtemperature and heat capacityeDPD particles
electroncharge and spin and eradiuselectronic force field
ellipsoidshape, quaternion, angular momentumaspherical particles
fullmolecular + chargebio-molecules
lineend points, angular velocityrigid bodies
mdpddensitymDPD particles
mesontmass, radius, length, buckling, connections, tube idmesoscopic nanotubes
molecularbonds, angles, dihedrals, impropersuncharged molecules
oxdnanucleotide polaritycoarse-grained DNA and RNA models
perimass, volumemesoscopic Peridynamic models
smdvolume, kernel diameter, contact radius, masssolid and fluid SPH particles
sphrho, esph, cvSPH particles
sphere尺寸,质量,角速度细粒度模型
spinmagnetic momentsystem with magnetic particles
tdpdchemical concentrationtDPD particles
templatetemplate index, template atomsmall molecules with fixed topology
tricorner points, angular momentumrigid bodies
wavepacketcharge, spin, eradius, etag, cs_re, cs_imAWPMD

原文链接:atom_style command — LAMMPS documentation

data文件中粒子的书写格式

angleatom-ID molecule-ID atom-type x y z
atomicatom-ID atom-type x y z
bodyatom-ID atom-type bodyflag mass x y z
bondatom-ID molecule-ID atom-type x y z
chargeatom-ID atom-type q x y z
dipoleatom-ID atom-type q x y z mux muy muz
dpdatom-ID atom-type theta x y z
edpdatom-ID atom-type edpd_temp edpd_cv x y z
electronatom-ID atom-type q spin eradius x y z
ellipsoidatom-ID atom-type ellipsoidflag density x y z
fullatom-ID molecule-ID atom-type q x y z
lineatom-ID molecule-ID atom-type lineflag density x y z
mdpdatom-ID atom-type rho x y z
mesontatom-ID molecule-ID atom-type bond_nt mass mradius mlength buckling x y z
molecularatom-ID molecule-ID atom-type x y z
periatom-ID atom-type volume density x y z
smdatom-ID atom-type molecule volume mass kradius cradius x0 y0 z0 x y z
sphatom-ID atom-type rho esph cv x y z
sphereatom-ID atom-type diameter density x y z
spinatom-ID atom-type x y z spx spy spz sp
tdpdatom-ID atom-type x y z cc1 cc2 … ccNspecies
templateatom-ID atom-type molecule-ID template-index template-atom x y z
triatom-ID molecule-ID atom-type triangleflag density x y z
wavepacketatom-ID atom-type charge spin eradius etag cs_re cs_im x y z
hybridatom-ID atom-type x y z sub-style1 sub-style2 …

PDB文件每列含义

说明
1 – 6记录类型
7 – 11原子序号
13 – 16原子名称,往往从第14位开始写, 占四个字符的原子名称才会从第13位开始写
17额外定位符
18 – 20残基名称
22原子所属的链
23 – 26残基序列号
27残基插入代码
28 – 30留空
31 – 38x坐标
39 – 46y坐标
47 – 54z坐标
55 – 60占有率
61 – 66温度因子
67 – 72留空
73 – 76区段标识
77 – 78元素符号, 右对齐
79 – 80原子电荷
PDB文件每列含义

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