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Re: [lammps-users] TIP4P-2005 water model
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Re: [lammps-users] TIP4P-2005 water model


From: Steve Plimpton <sjplimp@...24...>
Date: Mon, 14 Aug 2017 09:57:37 -0600

Please post to the list, not to me.
Originally you said this:

However, when I start, it just stays running while nothing happens on the screen no matter how long I wait.

Please look at the energies in your output, they blow up and
go to INF.  Thus the dynamics is wrong even after
20 steps.  So if you fix the dynamics and your model, then
LAMMPS will likely runfine.

Steve

On Mon, Aug 14, 2017 at 12:11 AM, XIAO <284237308@...1204...> wrote:

Step c_tp KinEng PotEng TotEng Volume Press v_waterpress v_den v_dh2o
       0            0            0   -7690.0708   -7690.0708         9261    305616.13     305696.1   0.86245551     862.4557
       1            0            0   -14760.946   -14760.946         9261    142884.92     142964.9   0.86245551     862.4557
       2            0            0   -18037.943   -18037.943         9261    123134.81    123214.78   0.86245551     862.4557
       3            0            0   -26598.338   -26598.338         9261    101385.15    101465.13   0.86245551     862.4557
       4            0            0   -110418.82   -110418.82         9261   -105446.05   -105366.07   0.86245551     862.4557
       5            0            0   -237442.67   -237442.67         9261   -418930.96   -418850.99   0.86245551     862.4557
       6            0            0   -1287851.2   -1287851.2         9261   -3011341.7   -3011261.7   0.86245551     862.4557
       7            0            0   -7748834.8   -7748834.8         9261    -18957043    -18956963   0.86245551     862.4557
       8            0            0    -66143752    -66143752         9261 -1.6307564e+08 -1.6307556e+08   0.86245551     862.4557
       9            0            0 -1.1696151e+09 -1.1696151e+09         9261 -2.8864417e+09 -2.8864416e+09   0.86245551     862.4557
      10            0            0 -2.7281112e+10 -2.7281112e+10         9261 -6.7329586e+10 -6.7329585e+10   0.86245551     862.4557
      11            0            0 -5.2431488e+10 -5.2431488e+10         9261 -1.2940069e+11 -1.2940069e+11   0.86245551     862.4557
      12            0            0 -1.1374683e+11 -1.1374683e+11         9261 -2.8072715e+11 -2.8072715e+11   0.86245551     862.4557
      13            0            0 -1.9453242e+11 -1.9453242e+11         9261 -4.801048e+11 -4.801048e+11   0.86245551     862.4557
      14            0            0 -5.4780619e+11 -5.4780619e+11         9261 -1.3519803e+12 -1.3519803e+12   0.86245551     862.4557
      15            0            0 -1.191004e+13 -1.191004e+13         9261 -2.9393316e+13 -2.9393316e+13   0.86245551     862.4557
      16            0            0 -4.0183392e+13 -4.0183392e+13         9261 -9.9189264e+13 -9.9189264e+13   0.86245551     862.4557
      17            0            0 -4.3085599e+14 -4.3085599e+14         9261 -1.0617783e+15 -1.0617783e+15   0.86245551     862.4557
      18            0            0 -9.2074509e+14 -9.2074509e+14         9261 -2.2590666e+15 -2.2590666e+15   0.86245551     862.4557
      19            0            0 -1.6161404e+15 -1.6161404e+15         9261 -3.9950881e+15 -3.9950881e+15   0.86245551     862.4557
      20            0            0 -4.0443943e+15 -4.0443943e+15         9261 -9.5627037e+15 -9.5627037e+15   0.86245551     862.4557
      21            0            0 -3.2101385e+16 -3.2101385e+16         9261 -8.8919033e+16 -8.8919033e+16   0.86245551     862.4557
      22            0            0         -inf         -inf         9261         -nan          nan   0.86245551     862.4557

    This is what I got when I set thermo 1.

    I'm quite confused about what is wrong in my script...


On 08/11/2017 10:58 PM, Steve Plimpton wrote:
which stage of the script is stalling?  your output
should tell you that.  If its the minimize, try running
with larger tolerance and or variable th=1

Steve

On Fri, Aug 11, 2017 at 1:49 AM, 284237308@...1204... <284237308@...1204...> wrote:
Hello guys,
    I'm trying my water model with TIP4P-2005. Here is my script.
    However, when I start, it just stays running while nothing happens on the screen no matter how long I wait.
    So, is there anything wrong about my script?
    Thanks.



#Pure water

units           real
dimension       3
boundary        p p p 
atom_style      full

read_data       267watercube.data 

#Force field parameters
#H=1, O=2 

set             type 1 charge 0.5564
set             type 2 charge -1.1128              

#TIP4P-2005 water
pair_style      lj/cut/tip4p/long 2 1 1 1 0.1546 13.0 8.5
pair_modify     tail yes mix arithmetic
bond_style      harmonic
angle_style     harmonic
kspace_style    pppm/tip4p 1.0e-5

pair_coeff      1 1 0.0 0.0         #H-H
pair_coeff      2 2 0.1852 3.1589   #O-O
pair_coeff      1 2 0.0 0.0         #O-H
bond_coeff      1 0.0 0.9572        #H-O
angle_coeff     1 0.0 104.52        #H-O-H

neighbor        3.0 bin
neigh_modify    every 1 delay 1 check yes

#Group
group           water type 1 2
group           oxgen type 2

#Calculations

compute         tp water temp 
compute         peratom water stress/atom NULL
compute         pr water reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
compute         pr3 water reduce sum c_peratom[4] c_peratom[5] c_peratom[6]

variable        T equal 300.0
variable        P equal 1.0
variable        dt equal 0.5
variable        ci equal 5                              #correlation interval
variable        si equal 2                              #sample interval
variable        ti equal ${ci}*${si}                    #total interval
variable        th equal 1000                           #thermo interval
variable        di equal 1000                           #dump interval
variable        Tdamp equal ${dt}*100
variable        Pdamp equal ${dt}*1000
variable        den equal density



#Run

timestep        ${dt}
thermo          ${th}
thermo_style    custom step c_tp ke pe etotal vol press v_den 

minimize        1.0e-4 1.0e-6 100 1000

fix             shakeh2o water shake 0.0001 200 0 b 1 a 1

fix             l all langevin ${T} ${T} ${Tdamp} 19930830
fix             e all nve 

dump            1 all atom ${di} langevin-nve.lammpstrj

run             10000

unfix           l
unfix           e 
undump          1


fix             1 all npt temp ${T} ${T} ${Tdamp} iso ${P} ${P} ${Pdamp}

dump            1 all atom ${di} npt.lammpstrj

run             10000

undump          1


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