安装及使用说明
- 安装fftw，用默认的双精度，下载地址
- Extract the contents of the compressed file into your favorite directory:
tar –zxof 2pt.tar.gz (on linux) - Make sure which compiler you have, g++ (in gnu) or icpc (in intel). Check whcich do you have by
g++ --versionoricpc --version. - Rename the Makefile.gnu or Makefile.intel into Makefile.
- Navigate to the 2pt/src directory and edit the Makefile to point to the location of the compiler.
- Navigate to the 2pt/src directory and edit the Makefile to point to the location of the FFTW3 library
- Type ‘make install’ in this directory. If all goes well you should have a binary called 2pt_analysis in the ../bin directory
- Create your control file
- Run the analysis using “{install_directory}/2pt/bin/2pt_analysis {control_file}”
需要准备的文件
- 结构文件,如lammps的data文件
- 轨迹文件 ，可用下文2PT模拟单独生成
- control文件，控制2PT分析用
- group文件（非必须）
用于2PT分析的MD模拟用IN文件
2PT_simu.in
units real
boundary p p p
dimension 3
atom_style full
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
pair_style lj/class2/coul/long 12.0
kspace_style pppm 1.0e-4
read_data polymers_w_stage_NPTfinal.data
pair_modify mix geometric
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
thermo_style multi
thermo_modify line multi format float %14.6f
variable sname index polymer_w
print "================================================"
print "NVT dynamics for 20ps dumping velocities"
print "================================================"
thermo 2
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol
thermo_modify line multi
fix 1 all nvt temp 300.0 300.0 100.0
dump 1 all custom 2 ${sname}.2pt.lammps id type xu yu zu vx vy vz
run 10000
undump 1
unfix 1
control文件
2pt.mol.in
IN_LMPDATA ./polymers_w_stage_NPTfinal.data
IN_LMPTRJ polymer_w.2pt
# IN_GROUPFILE 2pt.mol.grp # Unnecessary
ANALYSIS_FRAME_INITIAL 1
ANALYSIS_FRAME_FINAL 0
ANALYSIS_FRAME_STEP 1
ANALYSIS_VAC_CORLENGTH 0.5
ANALYSIS_VAC_MEMORYMB 8000
ANALYSIS_VAC_2PT 3
ANALYSIS_OUT polymer_w.2pt.mol
ANALYSIS_LMP_TSTEP 0.002
ANALYSIS_VAC_LINEAR_MOL 0
ANALYSIS_VAC_ROTN_SYMMETRY 2
ANALYSIS_VAC_FIXED_DF 648
ANALYSIS_SHOW2PT 1
group文件
2pt.mol.grp
Total Groups: 3
Group 1 Atoms 1300
1 - 1300
Group 2 Atoms 6678
1301 - 7978
Group 3 Atoms 12
7979 - 7990
手机版“神探玺洛克”请扫码
