Merge pull request #638 from jdevemy/master (65b295e8) · Commits · 郑智淋 / lammps

doc/src/Section_howto.txt

+2 −2

Original line number	Diff line number	Diff line
		@@ -2859,8 +2859,8 @@ The nature of the atoms (core, Drude particle or non-polarizable) is
		specified via the "fix drude"_fix_drude.html command. The special
		list of neighbors is automatically refactored to account for the
		equivalence of core and Drude particles as regards special 1-2 to 1-4
		screening. It may be necessary to use the {extra} keyword of the
		"special_bonds"_special_bonds.html command. If using "fix
		screening. It may be necessary to use the {extra/special/per/atom}
		keyword of the "read_data"_read_data.html command. If using "fix
		shake"_fix_shake.html, make sure no Drude particle is in this fix
		group.

examples/USER/drude/README

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Original line number	Diff line number	Diff line
		@@ -6,6 +6,9 @@ Nosé-Hoover or Langevin thermostats.

		* `butane` -- simulation in NVT ensemble with Thole damping

		* `toluene` -- simulation in NVT ensemble with Thole damping and
		use of the `extra/special/per/atom` keyword

		* `ethanol` -- simulation in NpT ensemble with Thole damping

		* `swm4-ndp` -- 4-site rigid water model in NpT ensemble (no Thole

examples/USER/drude/toluene/data.toluene

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File added.

Preview size limit exceeded, changes collapsed.

examples/USER/drude/toluene/in.toluene.lang

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Original line number	Diff line number	Diff line
		# 250 toluene system for drude polarizability example (Langevin)

		units real
		boundary p p p

		atom_style full
		bond_style harmonic
		angle_style harmonic
		dihedral_style opls
		improper_style opls
		special_bonds lj/coul 0.0 0.0 0.5

		pair_style lj/cut/thole/long 2.600 8.0 8.0
		pair_modify mix geometric tail yes
		kspace_style pppm 1.0e-4

		read_data data.toluene extra/special/per/atom 1

		comm_modify vel yes

		group gTOLUENE molecule 1:250
		group gCORES type 1 2 3 4 5 6 7
		group gDRUDES type 8 9 10 11 12

		pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
		pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
		pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
		pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
		pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
		pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
		pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
		pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
		pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
		pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
		pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
		pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
		pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
		pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
		pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
		pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
		pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
		pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
		pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
		pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
		pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
		pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
		pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
		pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
		pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
		pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
		pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
		pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
		pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
		pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
		pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
		pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
		pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
		pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
		pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
		pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
		pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
		pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
		pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
		pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
		pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
		pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
		pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
		pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
		pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
		pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
		pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
		pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
		pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
		pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
		pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
		pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
		pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
		pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
		pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
		pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
		pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
		pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
		pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
		pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
		pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
		pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
		pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
		pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
		pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
		pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
		pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
		pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT

		neighbor 2.0 bin

		variable vTEMP equal 260.0
		variable vTEMP_D equal 1.0
		variable vPRESS equal 1.0

		velocity gCORES create ${vTEMP} 12345
		velocity gDRUDES create ${vTEMP_D} 12345

		fix fDRUDE all drude C C C C C N N D D D D D

		fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8

		fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
		fix fNPH all nve

		compute cTEMP all temp/drude

		thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
		thermo 50

		timestep 0.5
		run 2000

examples/USER/drude/toluene/in.toluene.nh

0 → 100644

+122 −0

Original line number	Diff line number	Diff line
		# 250 toluene system for drude polarizability example (Nose-Hoover)

		units real
		boundary p p p

		atom_style full
		bond_style harmonic
		angle_style harmonic
		dihedral_style opls
		improper_style opls
		special_bonds lj/coul 0.0 0.0 0.5

		pair_style lj/cut/thole/long 2.600 8.0 8.0
		pair_modify mix geometric tail yes
		kspace_style pppm 1.0e-4

		read_data data.toluene extra/special/per/atom 1

		comm_modify vel yes

		group gTOLUENE molecule 1:250
		group gCORES type 1 2 3 4 5 6 7
		group gDRUDES type 8 9 10 11 12

		pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
		pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
		pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
		pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
		pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
		pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
		pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
		pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
		pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
		pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
		pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
		pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
		pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
		pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
		pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
		pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
		pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
		pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
		pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
		pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
		pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
		pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
		pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
		pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
		pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
		pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
		pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
		pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
		pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
		pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
		pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
		pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
		pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
		pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
		pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
		pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
		pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
		pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
		pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
		pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
		pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
		pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
		pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
		pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
		pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
		pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
		pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
		pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
		pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
		pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
		pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
		pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
		pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
		pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
		pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
		pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
		pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
		pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
		pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
		pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
		pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
		pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
		pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
		pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
		pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
		pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
		pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
		pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT


		neighbor 2.0 bin

		variable vTEMP equal 260.0
		variable vTEMP_D equal 1.0
		variable vPRESS equal 1.0

		velocity gCORES create ${vTEMP} 12345
		velocity gDRUDES create ${vTEMP_D} 12345

		fix fDRUDE all drude C C C C C N N D D D D D

		fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8

		compute cTEMP_CORE gCORES temp/com
		compute cTEMP all temp/drude

		fix fDIRECT all drude/transform/direct
		fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
		fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
		fix fINVERSE all drude/transform/inverse

		fix fMOMENTUM all momentum 100 linear 1 1 1

		thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
		thermo 50

		timestep 0.5
		run 2000

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