Temperature drops to zero in NVT with ReaxFF

I met this issue recently: Temperature drops to zero in NVT with ReaxFF.
If you happened to meet this problem too, the following tips you can try with:

(1) Always check the UNITs you used first.

(2) Try a shorter timestep, since the timestep in ReaxFF is normally 5-10 times shorter than the one you used in MD with other force functions.

(3) After relaxation of system (such as NPT), don't create the velocity again before next step (such as NVT). Since ReaxFF is very sensitive to the neighbor environment, if new velocity is introduced, its neighbor environment could be dramatically changed.

(4) While relaxing the system box with NPT, try to make the size of box change slowly. Dramatic change of box size will change the neighbor environment.

(5) In my case, the steps of my calculation is:  Create velocity at low temperature => Relax system with NPT => Create velocity with a higher temperature  => NVT => NVE.
    * If I skipped the NVT step,  the NVE step can run well.
    * If I skipped the Step of Creating a new velocity, the NVT step can run well.
   

Change sw potential and include packages in Lammps

• Change SW potential

1. Copy file pair_sw.cpp to ./lammps/src/  folder
2. Copy file Makefile.linux to ./lammps/src/MAKE/ folder
3. Copy fftw fold to ./lammps/ folder
#4. Go to folder ./lammps/src/
#5. make -j linux

• Include Phonon package in lammps

4. Go to website: http://code.google.com/p/fix-phonon/wiki/Install_with_LAMMPS
5. Go to folder src
   edit Makefile under src, append "user-phonon" to the variable "PACKUSER"
5. make yes-kspace
6. make yes-user-phonon

•  install meam library

7. $cd ./lammps/lib/meam/
8. $make -f Makefile.gfortran

•  install reax library

9. $cd ./lammps/lib/reax/
10. $make -f Makefile.gfortran

11. Go to folder ./lammps/src/
12. $make yes-meam
13. $make yes-reax

• include rebo potential

14.$make yes-manybody
15. $make -j linux



#some useful commands:  make package-status, make yes-all , make no-all, make clean-all, make package
#check which package/lib have been installed:
$ lmp_linux -h

Some commands for linux environmental variables

1. $ echo $SHELL
2. $ echo $PATH
3. $ setenv
4. $ vi .tcshrc
5. $ which xxx (command, such vmd, lammps...)

commands to check cpu information on Linux

http://www.binarytides.com/linux-cpu-information

CPU hardware information

 The cpu information includes details about the processor, like the architecture, vendor name, model, number of cores, speed of each core etc. There are quite a few commands on linux to get those details about the cpu hardware, and here is a brief about some of the commands. 

1. /proc/cpuinfo

The /proc/cpuinfo file contains details about individual cpu cores. Output its contents with less or cat.

$ less /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 23
model name      : Intel(R) Core(TM)2 Quad CPU    Q8400  @ 2.66GHz
stepping        : 10
microcode       : 0xa07
cpu MHz         : 1998.000
cache size      : 2048 KB
physical id     : 0
siblings        : 4
core id         : 0
cpu cores       : 4
apicid          : 0
initial apicid  : 0
fpu             : yes
fpu_exception   : yes
cpuid level     : 13
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm sse4_1 xsave lahf_lm dtherm tpr_shadow vnmi flexpriority
bogomips        : 5303.14
clflush size    : 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual
power management:

Every processor or core is listed separately the various details about speed, cache size and model name are included in the description.
To count the number of processing units use grep with wc

$ cat /proc/cpuinfo | grep processor | wc -l
4

The number of processors shown by /proc/cpuinfo might not be the actual number of cores on the processor. For example a processor with 2 cores and hyperthreading would be reported as a processor with 4 cores.

To get the actual number of cores, check the core id for unique values

$ cat /proc/cpuinfo | grep 'core id'
core id         : 0
core id         : 2
core id         : 1
core id         : 3

So there are 4 different core ids. This indicates that there are 4 actual cores.

2. lscpu

lscpu is a small and quick command that does not need any options. It would simply print the cpu hardware details in a user-friendly format.

$ lscpu
Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                4
On-line CPU(s) list:   0-3
Thread(s) per core:    1
Core(s) per socket:    4
Socket(s):             1
NUMA node(s):          1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 23
Stepping:              10
CPU MHz:               1998.000
BogoMIPS:              5303.14
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              2048K
NUMA node0 CPU(s):     0-3

3. hardinfo

Hardinfo is a gtk based gui tool that generates reports about various hardware components. But it can also run from the command line only if there is no gui display available.

$ hardinfo | less

It would produce a large report about many hardware parts, by reading files from the /proc directory. The cpu information is towards the beginning of the report. The report can also be written to a text file.
Hardinfo also performs a few benchmark tests taking a few minutes before the report is displayed.

4. lshw

The lshw command can display limited information about the cpu. lshw by default shows information about various hardware parts, and the '-class' option can be used to pickup information about a specific hardware part.

$ sudo lshw -class processor
  *-cpu                   
       description: CPU
       product: Intel(R) Core(TM)2 Quad CPU    Q8400  @ 2.66GHz
       vendor: Intel Corp.
       physical id: 0
       bus info: cpu@0
       version: Intel(R) Core(TM)2 Quad CPU    Q8400  @ 2.66GHz
       slot: LGA 775
       size: 1998MHz
       capacity: 4GHz
       width: 64 bits
       clock: 333MHz
       capabilities: fpu fpu_exception wp vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx x86-64 constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm sse4_1 xsave lahf_lm dtherm tpr_shadow vnmi flexpriority cpufreq

The vendor, model and speed of the processor are being shown correctly. However it is not possible to deduce the number of cores on the processor from the above output.

5. nproc

The nproc command just prints out the number of processing units available. Note that the number of processing units might not always be the same as number of cores.

$ nproc
4

6. dmidecode

The dmidecode command displays some information about the cpu, which includes the socket type, vendor name and various flags.

$ sudo dmidecode -t 4
# dmidecode 2.12
SMBIOS 2.4 present.

Handle 0x0000, DMI type 4, 35 bytes
Processor Information
        Socket Designation: LGA 775
        Type: Central Processor
        Family: Pentium D
        Manufacturer: Intel(R) Corporation
        ID: 7A 06 01 00 FF FB EB BF
        Signature: Type 0, Family 6, Model 23, Stepping 10
        Flags:
                FPU (Floating-point unit on-chip)
                VME (Virtual mode extension)
                DE (Debugging extension)
                PSE (Page size extension)
                TSC (Time stamp counter)
                MSR (Model specific registers)
                PAE (Physical address extension)
                MCE (Machine check exception)
                CX8 (CMPXCHG8 instruction supported)
                APIC (On-chip APIC hardware supported)
                SEP (Fast system call)
                MTRR (Memory type range registers)
                PGE (Page global enable)
                MCA (Machine check architecture)
                CMOV (Conditional move instruction supported)
                PAT (Page attribute table)
                PSE-36 (36-bit page size extension)
                CLFSH (CLFLUSH instruction supported)
                DS (Debug store)
                ACPI (ACPI supported)
                MMX (MMX technology supported)
                FXSR (FXSAVE and FXSTOR instructions supported)
                SSE (Streaming SIMD extensions)
                SSE2 (Streaming SIMD extensions 2)
                SS (Self-snoop)
                HTT (Multi-threading)
                TM (Thermal monitor supported)
                PBE (Pending break enabled)
        Version: Intel(R) Core(TM)2 Quad CPU    Q8400  @ 2.66GHz
        Voltage: 1.6 V
        External Clock: 333 MHz
        Max Speed: 4000 MHz
        Current Speed: 2666 MHz
        Status: Populated, Enabled
        Upgrade: Socket LGA775
        L1 Cache Handle: 0x0003
        L2 Cache Handle: 0x0001
        L3 Cache Handle: Not Provided
        Serial Number: Not Specified
        Asset Tag: Not Specified
        Part Number: Not Specified

7. cpuid

The cpuid command fetches CPUID information about Intel and AMD x86 processors.
The program can be installed with apt on ubuntu

$ sudo apt-get install cpuid

And here is sample output

$ cpuid

.....

Vendor ID: "GenuineIntel"; CPUID level 13

Intel-specific functions:
Version 0001067a:
Type 0 - Original OEM
Family 6 - Pentium Pro
Model 7 - Pentium III/Pentium III Xeon - external L2 cache
Stepping 10
Reserved 4

Extended brand string: "Intel(R) Core(TM)2 Quad CPU    Q8400  @ 2.66GHz"
CLFLUSH instruction cache line size: 8
Initial APIC ID: 2
Hyper threading siblings: 4

Feature flags bfebfbff:
FPU    Floating Point Unit
VME    Virtual 8086 Mode Enhancements
DE     Debugging Extensions
PSE    Page Size Extensions
TSC    Time Stamp Counter
MSR    Model Specific Registers
PAE    Physical Address Extension
MCE    Machine Check Exception
CX8    COMPXCHG8B Instruction
APIC   On-chip Advanced Programmable Interrupt Controller present and enabled
SEP    Fast System Call
MTRR   Memory Type Range Registers
PGE    PTE Global Flag
MCA    Machine Check Architecture
CMOV   Conditional Move and Compare Instructions
FGPAT  Page Attribute Table
PSE-36 36-bit Page Size Extension
CLFSH  CFLUSH instruction
DS     Debug store
ACPI   Thermal Monitor and Clock Ctrl
MMX    MMX instruction set
FXSR   Fast FP/MMX Streaming SIMD Extensions save/restore
SSE    Streaming SIMD Extensions instruction set
SSE2   SSE2 extensions
SS     Self Snoop
HT     Hyper Threading
TM     Thermal monitor
31     reserved

.....

8. inxi

Inxi is a script that uses other programs to generate a well structured easy to read report about various hardware components on the system. Check out the full tutorial on inxi.

$ sudo apt-get install inxi

Print out cpu/processor related information

$ inxi -C
CPU:       Quad core Intel Core2 Quad CPU Q8400 (-MCP-) cache: 2048 KB flags: (lm nx sse sse2 sse3 sse4_1 ssse3 vmx) 
           Clock Speeds: 1: 1998.00 MHz 2: 1998.00 MHz 3: 1998.00 MHz 4: 1998.00 MHz

Build Graphene with Material Studio

Build Graphene with Material Studio

 

1) File -> Import -> Structures -> ceramics -> graphite.msi;

2) Build -> Symmetry -> Make P1;

3) Remove one of the two layers;

4) Build -> Symmetry -> Find Symmetry -> Impose Symmetry;

5) Build -> Symmetry -> Supercell 2*2*2;

6) Build -> Crystals -> Rebuild Crystal -> Lattice Parameters -> a=4.26, b=2.46, c=25, alpha=beta=gamma=90 -> Rebuild;

7) Build -> Symmetry -> Supercell 5*5*1.

Access VirtualBox Shared Folder from Ubuntu 12.04 Guest Machine

 from:
http://www.liberiangeek.net/2012/05/access-virtualbox-shared-folder-from-ubuntu-12-04-precise-pangolin-guest-machine/


Using VirtualBox? And do you want to access shared folders on the host machine from the guest machine which has Ubuntu on it? Well, this brief tutorial is going to show you how to do that. This is a perfect way to get file located on the host machine to the guest machine which in this case is a Ubuntu machine.

This tutorial was done using Windows 7 as my host machine and Ubuntu 12.04 as the guest. Also, make sure you have access to the folder you’re sharing, or it won’t work.

Objectives:

• Access shared folders on the host from the guest machine using VirtualBox
• Enjoy!

To get started, select the virtual machine to wish to configure then click ‘Settings’ and select the shared folder on the left menu. Click ‘Add’ the select the the folder to share.



Login to Ubuntu and run the commands below to add your user account into VirtualBox account group.

sudo adduser <username> vboxsf

Next, logout or restart your computer and go to the /media/ folder to access the shared folder.



Enjoy!

How to generate LAMMPS data file with force field parameters

http://sunghoedwardkim.blogspot.sg/2011/04/how-to-generate-lammps-data-file-with.html

To make LAMMPS data file using pdb file in VMD,

1. load pdb file (or any molecule configuration file) in VMD

2. in VMD command line, type
topo writelammpsdata filename type
# type : full, atomic, etc..

3. a data file with filename is created in VMD folder




To make LAMMPS data file with force field parameters, "msi2lmp", a LAMMPS tool (/tools/msi2lmp/) can be used.

1. build msi2lmp
make   in /tools/msi2lmp/src/

2. msi2lmp.exe, force field file (e.g., cvff.frc), car and mdf files should be in same directory.
msi2lmp.exe rootname -class I -frc force_field_name
# rootname.cat
# rootname.mdf
# -class I (e.g, cvff), -class II (e.g., CFFx)
# -frc cvff   (cvff.frc)