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[lammps-users] Fwd: Regarding Tersoff and Eam pot.
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[lammps-users] Fwd: Regarding Tersoff and Eam pot.


From: Sharma MD <sa.md.dtm@...24...>
Date: Mon, 21 Aug 2017 14:07:44 +0530


---------- Forwarded message ----------
From: Sharma MD <sa.md.dtm@...24...>
Date: Sun, Aug 20, 2017 at 1:46 PM
Subject: Re: [lammps-users] Regarding Tersoff and Eam pot.
To: Axel Kohlmeyer <akohlmey@...24...>


Thank you for suggestion.
I used Be as Substrate material and Diamond as tool. Be is HCP and Diamond has cubic diamond structure. substrate has 3 layers of atoms: rigid layer at bottom, thermostat layer in the middle and newton layer at the top. Similarly for Diamond. rigid layer is for supporting the structure and thermo layer for diffusing the heat generated in the cutting zone and newton layer for actual dynamics of system. Thermo + Newton layer together forms mobile layer on which NVE dynamics is employed.
First the equilibration is carried out on this mobile layer at 293K for 10 ps before cutting starts. However, error occurs.

Files are attached. Kindly suggest.

On Sat, Aug 19, 2017 at 6:58 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Sat, Aug 19, 2017 at 9:12 AM, Sharma MD <sa.md.dtm@...36.....24...> wrote:
It happened in the very first step.

System was fine.

there must be something bogus in your input that causes the overflow of the memory allocation during neighbor list setup.
but you are not providing sufficient information, so there is no way to track this down.

if you want to get constructive help, you have to follow the mailing list guidelines and provide sufficient information and detail
 

On Sat, Aug 19, 2017 at 5:35 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.


#### Program in Box units
#echo screen
units metal
#newton on
dimension	3
boundary	m m p
atom_style	atomic
neighbor	2 bin
neigh_modify	delay 2 

# create geometry
#lattice hcp 2.284568182   
   
variable a equal 2.312646565
variable b equal $a
variable c equal $a*1.5682

lattice custom 1.0 a1 $a 0.0 0.0&
 a2 0.0 $b 0.0&
 a3 0.0 0.0 $c&
 basis 0.0 0.0 0.0& 
 basis 0.5 0.5 0.0& 
 basis 0.0 0.33333333 0.5& 
 basis 0.5 0.83333333 0.5
  
variable f equal 3
variable xi equal 0
variable xm equal 200
variable yi equal 20
variable ym equal 80
variable zi equal -30.8423
variable zm equal 30.8423
#variable zlo equal -25
#variable zhi equal 25

region s_box block 0 280 20 120 $(v_zi) $(v_zm) units box    # Simulation box 
create_box 6 s_box        # no. of atom types in box

region		work_new block $(v_xi+2*v_f) $(v_xm) $(v_yi+2*v_f) $(v_ym) $(v_zi) $(v_zm) units box
region		lt_fix block $(v_xi) $(v_xi+v_f) $(v_yi) $(v_ym) $(v_zi) $(v_zm) units box
region		bt_fix block $(v_xi) $(v_xm) $(v_yi) $(v_yi+v_f) $(v_zi) $(v_zm) units box
region 		work_boundary union 2 lt_fix bt_fix 

region		lt_therm	block $(v_xi+v_f) $(v_xi+2*v_f) $(v_yi+v_f) $(v_ym) $(v_zi) $(v_zm) units box
region		bt_therm	block $(v_xi+v_f) $(v_xm)  $(v_yi+v_f) $(v_yi+2*v_f) $(v_zi) $(v_zm) units box
region		work_thermostat union 2 lt_therm bt_therm
region 		workpiece union 3 work_new work_thermostat work_boundary

#lattice	fcc 3.6327 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
create_atoms	1 region workpiece

########create tool geometry

lattice diamond 3.562106  # for Diamond
variable a equal 3.562106 
variable R equal 20	             ##tool edge radius = R 
variable Rc1 equal  240
variable Rc2 equal   80          ## tool edge centre coordinates 
variable zlo equal -20
variable zhi equal  20
variable fc equal   3          ### fixed constant to make distance 3 Armstrong


#### Flank plane parameters

variable f11 equal   $(v_Rc1 + v_R * sin(PI/18))
variable f12 equal   $(v_Rc2 - v_R * cos(PI/18))
variable f13 equal    15
variable f14 equal   $(-v_R * sin(PI/18)) 
variable f15 equal   $(v_R * cos(PI/18)) 
variable f16 equal    0

## 1st (upper) Block parameters

variable B11 equal    $(v_Rc1 - v_R) 
variable B12 equal    $(v_Rc1 + v_R * 2) 
variable B13 equal    $(v_Rc2) 
variable B14 equal    $(v_Rc2 + v_R * 2) 
variable B15 equal    $(v_zlo)
variable B16 equal    $(v_zhi)

## 2nd (lower) Block paramers

variable B21 equal    $(v_Rc1) 
variable B22 equal    $(v_Rc1 + v_R*2)
variable B23 equal    $(v_Rc2 - v_R) 
variable B24 equal    $(v_Rc2)
variable B25 equal    $(v_zlo)
variable B26 equal    $(v_zhi)

## ToolThemo-upper_block parameters(TB1)
variable TT11 equal   $(v_Rc1 - v_R) 
variable TT12 equal   $(v_Rc1 + v_R*2 + v_fc) 
variable TT13 equal   $(v_Rc2 + v_R*2) 
variable TT14 equal   $(v_Rc2 + v_R*2 + v_fc) 
variable TT15 equal    $(v_zlo)
variable TT16 equal    $(v_zhi)

## ToolBoundary-upper_block parameters(BB1) 
variable TB11 equal    $(v_Rc1 - v_R) 
variable TB12 equal    $(v_Rc1 + v_R*2 + v_fc + v_fc)
variable TB13 equal    $(v_Rc2 + v_R*2+ v_fc) 
variable TB14 equal    $(v_Rc2 + v_R*2 + v_fc + v_fc) 
variable TB15 equal   $(v_zlo)
variable TB16 equal   $(v_zhi)

## ToolThemo-right_block parameters(TB2)
variable TT21 equal    $(v_Rc1 + v_R*2) 
variable TT22 equal    $(v_Rc1 + v_R*2 + v_fc) 
variable TT23 equal    $(v_Rc2 - v_R) 
variable TT24 equal    $(v_Rc2 + v_R*2 + v_fc) 
variable TT25 equal   $(v_zlo)
variable TT26 equal   $(v_zhi)


## ToolBoundary-right_block parameters(BB2) 
variable TB21 equal   $(v_Rc1 + v_R*2 + v_fc)
variable TB22 equal   $(v_Rc1 + v_R*2 + v_fc + v_fc)
variable TB23 equal   $(v_Rc2 - v_R)
variable TB24 equal   $(v_Rc2 + v_R*2 + v_fc + v_fc)
variable TB25 equal   $(v_zlo)
variable TB26 equal   $(v_zhi)


region 	    tool_edge cylinder z ${Rc1} ${Rc2} $R $(v_zlo) $(v_zhi) units box

region      flank plane ${f11} ${f12}  ${f13} ${f14} ${f15} ${f16} units box

region      box1 block ${B11} ${B12} ${B13} ${B14} $(v_zlo) $(v_zhi) units box
region      box2 block ${B21} ${B22} ${B23} ${B24} $(v_zlo) $(v_zhi) units box

region 		tool_boundary1 block ${TB11} ${TB12} ${TB13} ${TB14} $(v_zlo) $(v_zhi) units box
region 		tool_boundary2 block ${TB21} ${TB22} ${TB23} ${TB24} $(v_zlo) $(v_zhi) units box
region 		tool_thermo1 block ${TT11} ${TT12} ${TT13} ${TT14} $(v_zlo) $(v_zhi) units box
region 		tool_thermo2 block ${TT21} ${TT22} ${TT23} ${TT24} $(v_zlo) $(v_zhi) units box


region tool_boundary union 2 tool_boundary1 tool_boundary2
region tool_thermo  union 2 tool_thermo1 tool_thermo2  

region tool_thermoboundary union 2 tool_boundary tool_thermo

#region tool_new1 intersect 3 tool_box  flank  rake              # tool newtonian atoms
region tool_123  union 3 tool_edge box1 box2

region tool_new intersect 2  tool_123 flank
#region tool_outlayer1 intersect 2 tool_thermoboundary flank    ##tool - thermo+boundary
#region tool_outlayer2 intersect 2 tool_thermoboundary rake
region tool_outlayer intersect 2 tool_thermoboundary flank 

region tool union 2 tool_new tool_outlayer                   ### whole tool
region tool_mobile union 2 tool_new tool_thermo         ## tool - newtonian+ thermo for nve dynamics

create_atoms	2 region tool


mass		1 9.012182 
mass		2 9.012182  
mass		3 9.012182 
mass		4 12.0107
mass		5 12.0107
mass		6 12.0107

###Assign Groups to various regions
group T_bound region tool_boundary
group T_thermo region tool_thermo
group T_new region tool_new
group T_mobile region tool_mobile
group tool region tool

group w_bound region work_boundary
group w_thermo  region work_thermostat
group w_new  region work_new
group w_mobile  union  w_thermo  w_new
group work region workpiece

group TW_bound union T_bound w_bound
group TW_thermo union T_thermo w_thermo 
###group TW_mobile union T_mobile w_mobile    ## tool-w/p newtonian +thermo 
group TW_newton union T_new w_new          # tool and work Newtonian layer
group mobile subtract all TW_bound          # tool+work without boundary

###### set group as particular type
set group w_bound type 1
set group w_thermo type  2
set group w_new type 3

set group T_bound type 4
set group T_thermo type 5
set group T_new type 6
#set group tool type 4

############# compute temp. per atom as well as of region

variable kB equal  1.3806504e-23/1.602e-19    ######Boltzmann's const. and eV for metal units               
compute keperatom all ke/atom
variable tempatom atom c_keperatom*(2/3)/(v_kB)
#### dump variable as dump custom id v_tempatom

compute  temp_tool tool  temp
compute  temp_work work temp  
compute  temp_toolnew T_new temp
compute  temp_worknew w_new temp
compute  new mobile temp
compute  temp_all all temp 


thermo_style    custom step elapsed temp  press time  etotal pe ke  

######Interatomic Potential

pair_style hybrid tersoff eam/alloy morse 1.75
#pair_coeff * * BeC.tersoff Be Be Be C C C
pair_coeff * * tersoff  C.abop.tersoff NULL NULL NULL C C C
pair_coeff * * eam/alloy BeAgrawal.eam.alloy Be Be Be NULL NULL NULL 
pair_coeff 1*3 4*6 morse 2.566 1.7798 1.666  


#######Dynamics
timestep	0.001

velocity 	mobile create 293 58142275 temp new

fix 1 TW_bound setforce 0.0 0.0 0.0           ## boundary atoms of workpiece
fix 2 all nve
fix 3 mobile temp/rescale 5 293 293 0.05 1.00    ####thermal scaling/equilibration
fix_modify	3 temp new



#thermo 1                          ###Change
thermo		1000
	
thermo_modify	temp new
dump 1 all custom 10 alleq.*.dump id type x y z vx vy vz fx fy fz    
#dump 1 all custom 1 alleq.*.dump id type x y z vx vy vz fx fy fz v_tempatom       ###Change

#run 1                      ###Change
run		10000

Attachment: BeAgrawal.eam.alloy
Description: Binary data

Attachment: BeC.tersoff
Description: Binary data

Attachment: C.abop.tersoff
Description: Binary data