Micro and Nano Mechanics Group - User contributions [en]

MEAM Potential for Au-Ge

2016-12-27T08:27:58Z

Adrianos:

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Dec, 2016


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here:

http://micro.stanford.edu/wiki/MEAM_Potential_for_Au-Si

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 1.5228 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 1.5228 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai,'''25''', 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

==Benchmark in MD++==

Compile the code using the following command.

make meam-lammps build=R SYS=gpp

Use the following command to compute the equilibrium lattice constant and cohesive energy of pure Au (FCC). You can download the [[media:ge_au_benchmark.tcl.txt |ge_au_benchmark.tcl]] from the link.

The script calculates cohesive energy of Ge(DC), Au(Au), AuGe(B1), impurity energy of Au atom
in Ge DC and impurity energy of Ge atom in Au FCC.

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 0

The results are:

Ecoh Ge = -3.85 eV

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 1

Ecoh Au = -3.93 eV

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 2

Ecoh AuGe = -3.819 eV

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 5

Eimp Ge atom in Au FCC = 0.331 eV

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 6

Eimp Au atom in Ge DC = 1.3869 eV

MEAM Potential for Au-Ge

2016-12-27T08:27:15Z

Adrianos:

MEAM Potential for Au-Ge

2016-12-27T08:24:40Z

Adrianos: /* Benchmark in MD++ */

File:Ge au benchmark.tcl.txt

2016-12-27T08:14:32Z

Adrianos:

MEAM Potential for Au-Ge

2016-12-27T08:14:07Z

Adrianos: /* Benchmark in MD++ */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Dec, 2016


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here:

http://micro.stanford.edu/wiki/MEAM_Potential_for_Au-Si

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 1.5228 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 1.5228 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai,'''25''', 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

==Benchmark in MD++==

Compile the code using the following command.

make meam-lammps build=R SYS=gpp

Use the following command to compute the equilibrium lattice constant and cohesive energy of pure Au (FCC). You can download the [[media:ge_au_benchmark.tcl.txt |ge_au_benchmark.tcl]] from the link.

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 1

The results are

a0 = xxx Angstrom
Ecoh = xxx eV

Use the following command to compute the equilibrium lattice constant and cohesive energy of pure Ge (DC).

bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 0

The results are

a0 = xxx Angstrom
Ecoh = xxx eV

Use the following command to compute the equilibrium lattice constant and cohesive energy of Au-Ge (B1).

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 2

The results are

a0 = xxx Angstrom
Ecoh = xxx eV

===Impurity energy===

Use the following command to compute the impurity of a Au atom in Ge DC lattice.

bin/meam-lammps_gpp scripts/work/ge_au/si_au_benchmark.tcl 4

Mention paper....

MEAM Potential for Au-Ge

2016-12-27T03:05:27Z

Adrianos:

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Dec, 2016


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here:

http://micro.stanford.edu/wiki/MEAM_Potential_for_Au-Si

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 1.5228 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 1.5228 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai,'''25''', 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

==Benchmark in MD++==

Compile the code using the following command.

make meam-lammps build=R SYS=gpp

Use the following command to compute the equilibrium lattice constant and cohesive energy of pure Au (FCC). You can download the [[media:si-au.tcl.txt | si-au.tcl]] from the link.

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 1

The results are

a0 = xxx Angstrom
Ecoh = xxx eV

Use the following command to compute the equilibrium lattice constant and cohesive energy of pure Ge (DC).

bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 0

The results are

a0 = xxx Angstrom
Ecoh = xxx eV

Use the following command to compute the equilibrium lattice constant and cohesive energy of Au-Ge (B1).

bin/meam-lammps_gpp scripts/work/ge_au/ge_au_benchmark.tcl 2

The results are

a0 = xxx Angstrom
Ecoh = xxx eV

===Impurity energy===

Use the following command to compute the impurity of a Au atom in Ge DC lattice.

bin/meam-lammps_gpp scripts/work/ge_au/si_au_benchmark.tcl 4

Mention paper....

MEAM Potential for Au-Ge

2016-12-27T02:42:48Z

Adrianos:

MEAM Potential for Au-Ge

2016-12-27T02:36:04Z

Adrianos: /* MEAM Potential for Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here:

http://micro.stanford.edu/wiki/MEAM_Potential_for_Au-Si

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 1.5228 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 1.5228 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai,'''25''', 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

MEAM Potential for Au-Ge

2016-12-27T02:35:50Z

Adrianos: /* MEAM Potential for Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here:

http://micro.stanford.edu/wiki/MEAM_Potential_for_Au-Si

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 1.5228 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai,'''25''', 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

MEAM Potential for Au-Ge

2016-12-27T02:34:24Z

Adrianos: /* Original MEAM Potential for Au */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here:

http://micro.stanford.edu/wiki/MEAM_Potential_for_Au-Si

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 0.9858 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai,'''25''', 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

MEAM Potential for Au-Ge

2016-12-27T02:17:21Z

Adrianos: /* Cross Potential between Au and Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here
JUST REFER TO OTHER PAGE....!

UNDER CONSTRUCTION!!!!!

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 0.9858 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai,'''25''', 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

MEAM Potential for Au-Ge

2016-12-27T02:15:59Z

Adrianos: /* Cross Potential between Au and Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here
JUST REFER TO OTHER PAGE....!

UNDER CONSTRUCTION!!!!!

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 0.9858 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Same values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai,'''25''', 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

MEAM Potential for Au-Ge

2016-12-27T02:14:31Z

Adrianos: /* Cross Potential between Au and Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here
JUST REFER TO OTHER PAGE....!

UNDER CONSTRUCTION!!!!!

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 0.9858 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Same values are found in Table 3 of "AuGe mean potential fitted to the binary phase diagram", Yanming Wang, Adriano Santana and Wei Cai, 25, 025004, (2017)

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

MEAM Potential for Au-Ge

2016-12-27T02:10:23Z

Adrianos: /* Cross Potential between Au and Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here
JUST REFER TO OTHER PAGE....!

UNDER CONSTRUCTION!!!!!

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 0.9858 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of Ryu and Cai, J. Phys. Condens. Matter, 22, 055401 (2010).

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

MEAM Potential for Au-Ge

2016-12-27T02:06:04Z

Adrianos: /* Cross Potential between Au and Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here
JUST REFER TO OTHER PAGE....!

UNDER CONSTRUCTION!!!!!

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 0.9858 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of Ryu and Cai, J. Phys. Condens. Matter, 22, 055401 (2010).

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.70 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 2.0 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 4.722</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 0.989 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.180 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

MEAM Potential for Au-Ge

2016-12-27T02:04:19Z

Adrianos: /* Cross Potential between Au and Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here
JUST REFER TO OTHER PAGE....!

UNDER CONSTRUCTION!!!!!

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 0.9858 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of Ryu and Cai, J. Phys. Condens. Matter, 22, 055401 (2010).

re(1,2) = 2.67 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.4219 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.168 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.95 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 1.85 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 4.722</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 0.989 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.180 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T17:16:33Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Si MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.
For example, if you install MD++ on your local computer inside a home folder called "~/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in the "meamf" and "AuSi2nn.meam" files. If you want to run a Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also need to change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
</pre>

To run the simulation you need to to have installed and compiled MD++ and the potential you
want. In this case in the MD++ bin folder you must have the ausi meam-lammps executable.

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl $n $name $temp $Xsi
</pre>

where $n is the status number, 3, is to create a new structure. $name is just a file name to your choice. $temp is the temperature at which it will be created and $Xsi is the Silicon fraction in the droplet. For example, if you want to create a new structure with the name '1_700_45' at 700K and a silicon fraction of 45% then type:

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl 3 1_700_45 700 45
</pre>

if you know check the folder /Codes/MD++/runs there you will see the folder
/1_700_45_3

===Visualize input file===

Talk about visualizing the LAMMPS input file with OVITO, etc.

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T17:01:32Z

Adrianos:

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Si MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.
For example, if you install MD++ on your local computer inside a home folder called "~/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in the "meamf" and "AuSi2nn.meam" files. If you want to run a Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also need to change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
</pre>

To run the simulation you need to to have installed and compiled MD++ and the potential you
want. In this case in the MD++ bin folder you must have the ausi meam-lammps executable.

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl $n $name $temp $Xsi
</pre>

where $n is the status number, 3, is to create a new structure. $name is just a file name to your choice. $temp is the temperature at which it will be created and $Xsi is the Silicon fraction in the droplet. For example, if you want to create a new structure with the name '1_700_45' at 700K and a silicon fraction of 45% then type:

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl 3 1_700_45 700 45
</pre>

if you know check the folder /Codes/MD++/runs there you will see the folder
/1_700_45_3
===Visualize input file===

Talk about visualizing the LAMMPS input file with OVITO, etc.

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T16:58:51Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Si MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.
For example, if you install MD++ on your local computer inside a home folder called "~/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in the "meamf" and "AuSi2nn.meam" files. If you want to run a Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also need to change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
</pre>

To run the simulation you need to to have installed and compiled MD++ and the potential you
want. In this case in the MD++ bin folder you must have the ausi meam-lammps executable.

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl $n $name $temp $Xsi
</pre>

where $n is the status number, 3, is to create a new structure. $name is just a file name to your choice. $temp is the temperature at which it will be created and $Xsi is the Silicon fraction in the droplet. For example, if you want to create a new structure with the name '1_700_45' at 700K and a silicon fraction of 45% then type:

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl 3 1_700_45 700 45
</pre>

if you know check the folder /Codes/MD++/runs there you will see the folder
/1_700_45_3

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T16:54:51Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.
For example, if you install MD++ on your local computer inside a folder called "/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in "meamf" and "AuSi2nn.meam" files. If you wanted to run Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
</pre>

To run the simulation you need to to have installed and compiled MD++ and the potential you
want. In this case in the MD++ bin folder you must have the ausi meam-lammps executable.

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl $n $name $temp $Xsi
</pre>

where $n is the status number, 3, to create a new structure. $name is just a filename to your choice. $temp is the temperature at which it will be created and $Xsi is the Silicon fraction in the droplet. For example, if you want to create a new structure with the name '1_700_45' at 700K and a silicon fraction of 45% then type:

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl 3 1_700_45 700 45
</pre>

if you know check the folder /Codes/MD++/runs there you will see the folder
/1_700_45_3

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T16:53:13Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.
For example, if you install MD++ on your local computer inside a folder called "/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in "meamf" and "AuSi2nn.meam" files. If you wanted to run Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
>/pre>

To run the simulation you need to to have installed and compiled MD++ and the potential you
want. In this case in the MD++ bin folder you must have the ausi meam-lammps executable.

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl $n $name $temp $Xsi
</pre>

where $n is the status number, 3, to create a new structure. $name is just a filename to your choice. $temp is the temperature at which it will be created and $Xsi is the Silicon fraction in the droplet. For example, if you want to create a new structure with the name '1_700_45' at 700K and a silicon fraction of 45% then type:

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl 3 1_700_45 700 45
</pre>

if you know check the folder /Codes/MD++/runs there you will see the folder
/1_700_45_3

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T16:52:04Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.
For example, if you install MD++ on your local computer inside a folder called "/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in "meamf" and "AuSi2nn.meam" files. If you wanted to run Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
>/pre>

To run the simulation you need to to have installed and compiled MD++ and the potential you
want. In this case in the MD++ bin folder you must have the ausi meam-lammps executable.

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl $n $name $temp $Xsi
>/pre>

where $n is the status number, 3, to create a new structure. $name is just a filename to your choice. $temp is the temperature at which it will be created and $Xsi is the Silicon fraction in the droplet. For example, if you want to create a new structure with the name '1_700_45' at 700K and a silicon fraction of 45% then type:

<pre>
meam-lammps /Codes/work/ausi/si_au_md.tcl 3 1_700_45 700 45
>/pre>

if you know check the folder /Codes/MD++/runs there you will see the folder
/1_700_45_3

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T16:43:38Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.
For example, if you install MD++ on your local computer inside a folder called "/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in "meamf" and "AuSi2nn.meam" files. If you wanted to run Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
>/pre>

<pre>
talk about temperature, meaning of important lines
</pre>

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T16:42:38Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.
For example, if you install MD++ on your local computer inside a folder called "/Codes" you need to set the path to "meamfile" and "meafile". 'AuBt' 'Si4' are the label names for Au and Si which refer to a line in "meamf" and "AuSi2nn.meam" files. If you wanted to run Au/Ge instead of Au/Si simulation then you could use 'Ge5' instead of 'Si4' and also change the file AuSi2nn.meam for AuGe2nn.meam and the path to meafile accordingly.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
>/pre>

<pre>
explaine how the script works, Temperature, meaning of important lines
</pre>

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T16:35:00Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.

<pre>
#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/WORKSPACE/yanmingw/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/WORKSPACE/yanmingw/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps
>/pre>

<pre>
explaine how the script works, Temperature, meaning of important lines
</pre>

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T13:29:30Z

Adrianos: /* Create 3D structures */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script:
[[media:si_au.md.txt | si_au.md.tcl]]

This script is lengthy and can be used for multiple purposes. Here briefly we discuss relevant parts.
The section proc readmeam-lammps sets the description of where to find the relevant MEAM files
needed for the meam-lammps potential.

#------------------------------------------------------------
proc readmeam-lammps {} {
MD++ {
meamfile = "~/WORKSPACE/yanmingw/Codes/MD++/potentials/MEAMDATA/meamf"
meafile = "~/WORKSPACE/yanmingw/Codes/MD++/potentials/MEAMDATA/AuSi2nn.meam"
nspecies=2 element0="AuBt" element1="Si4" rcut = 4.5 readMEAM
NNM=3000
}
}
#end of proc readmeam-lammps

<pre>
explaine how the script works, Temperature, meaning of important lines
</pre>

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===Plot data===

 '''to highlitght sth'''

File:Si au.md.txt

2016-12-14T13:23:38Z

Adrianos:

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T13:21:58Z

Adrianos: /* Create 3D structures */

Classical Simulation of GeAu droplet on Ge substrate

2016-12-14T12:58:41Z

Adrianos:

Classical Simulation of GeAu droplet on Ge substrate

2016-12-04T11:34:23Z

Adrianos: /* Free Energy */

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script..

<pre>
explaine how the script works, Temperature, meaning of important lines
</pre>

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Data analysis===

After LAMMPS has finished the simulation there will be a certain (usually large) amount of
dump files with the form (dump*.md). Each of these files has the Cartesian coordinates of the
system for each time step throughout the whole run. Typically you will have about 1000 files to analyze although the output of dump files can be regulated.

With this raw data several observables can be calculated; surface growth versus simulation time,
histogram through the z axis even 3D movies of the surface growth. We explain how to calculate them with the help of the following MATLAB scripts:

===AuSi binary alloy===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the third argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

===Plot binary phase diagram===

Finally, place in the same folder all the *.dat files from the previous simulations,
Au with Si impurity, Si with Au impurity and the AuSi files for for the binary alloy
with the range of compositions. you'll also need these three scripts:
plot_liquid_free_energy.m, comtan.m and polyfunc.m create

Launch MATLAB and run plot_liquid_free_energy.m and you should get
the binary phase diagram.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-04T11:28:26Z

Adrianos: /* Create 3D structures */

Classical Simulation of GeAu droplet on Ge substrate

2016-12-04T11:25:42Z

Adrianos:

Molecular Dynamics simulations of Semiconductor Nanowires
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016

 '''Under Construction!!!''' 

This tutorial discusses the simulation procedure to study semiconductor nanowire or surface growth of a liquid binary alloy on top a solid substrate. As a step-by-step process the structures are created with MD++, classically simulated with molecular dynamics (LAMMPS) and the dump files from the simulation are further studied with different MATLAB scripts in order to plot velocity growth, histogram growth at the interface, 3D movie creation, etc. As an example, we will explain this procedure to simulate AuGe liquid droplet deposition on crystalline Ge substrate for different temperatures and initial molar fraction of Ge in the liquid.

===Create 3D structures===

The first step is to create the structures (LAMMPS input file) that will be employed
for the molecular dynamics. This can be easily achieved with MD++ providing a suitable
potential is available. In this case we would need to have the an Au-Ge MEAM potential
and the following TCL script..

<pre>
explaine how the script works, Temperature, meaning of important lines
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

===Run molecular dynamics simulations===

Once MD++ has completed there will be a file in the /runs folder. It will look
something like this:

<pre>
file1.lammps.gz
</pre>

which is the compressed form of the input file for LAMMPS (only cartesian coordinates)

We will place this file in a new folder with these files for the potential: meamf, library.meam
and the LAMMPS file run.in which has important parameters and refers to the file1.lammps file.

We explain the content run.in here and how to run it...

===Free Energy===
Simultaneously one can also calculate the free energy of Si-DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi binary alloy===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the third argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

===Plot binary phase diagram===

Finally, place in the same folder all the *.dat files from the previous simulations,
Au with Si impurity, Si with Au impurity and the AuSi files for for the binary alloy
with the range of compositions. you'll also need these three scripts:
plot_liquid_free_energy.m, comtan.m and polyfunc.m create

Launch MATLAB and run plot_liquid_free_energy.m and you should get
the binary phase diagram.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Classical Simulation of GeAu droplet on Ge substrate

2016-12-04T11:18:24Z

Adrianos: /* Create 3D structures */

MEAM Potential for Au-Si

2016-12-04T11:08:11Z

Adrianos: /* New 2nn MEAM Potential for Au */

MEAM Potential for Au-Si
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Si MEAM potential in MD++. It starts with the parameters in pure Au and pure Si potentials, then talks about the Au-Si cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

As an example, we first describe the original 'Au' potential whose parameters are given in M. I. Baskes, Phys. Rev. B 46, 2727 (1992).

The main parameters in the MEAM potential is specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines correspond to 'Au' is given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Au' 'fcc' 12. 79 196.967 6.34090112 5.449 2.20 6 2.20

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Au}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
4.07 3.93 1.04 1.0 1.58956328 1.50776392 2.60609758 1. 3

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' / <math>\sqrt{2}</math>.

<math>\rho_0^{\rm Au}</math> = '''rozero''' will be important only for cross-potential.

'''ibar''' is a setting used in the equation of state (EOS). It selects the
G(gamma) function in Eq (4) and (5) on the paper by BJ LEE: Phys. Rev. B 64, 184102 (2001)

While the functional form is quite different, the modulus is almost not affected by
the choice of ibar.

===New 2nn MEAM Potential for Au===

We now explain the newer 2nn MEAM potential whose parameters are given by Lee, Shim and Baskes, Phys. Rev. B 68, 144112 (2003), and later modified by Ryu and Cai, J. Phys. Condens. Matter 22, 055401 (2010).

The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines which correspond to 'AuBt' are given below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'AuBt' 'fcc' 12. 79 196.967 6.59815965 5.77 2.20 6.0 2.20

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Au}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
4.073 3.93 1.00 1.0 1.7 1.64 2.0 1. 3

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' / <math>\sqrt{2}</math>.

We can see that from 'Au' to 'AuBt', the following parameters are changed. The new parameters correspond to values given in Table I of Lee, Shim and Baskes, PRB (2003).

<math>\alpha</math> <math>\beta_i^{(0)}</math> <math>A_i</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math>
'Au' 6.34090112 5.449 1.04 1.58956328 1.50776392 2.60609758
'AuBt' 6.59815965 5.77 1.00 1.7 1.64 2.0

Note that in Table I of Lee et al. (2003), <math>t^{(1)} = 2.90</math>, while in the '''meamf''' file, t1 = 1.7. This is because of the '''augt1''' parameter. In '''meam_setup_done.F''', there is a line

t1_meam(:) = t1_meam(:) + augt1 * 3.d0/5.d0 * t3_meam(:)

This means that if '''augt1''' = 1.0, then the ''true'' value of t1 is 1.7 + 0.6 * 2.0 = 2.9.

'''augt1''' is specified in the '''AuSi2nn.meam''' file, as described below.

The '''AuSi2nn.meam''' file contains several lines that are relevant for the pure Au potential. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(1,1) = -0.182 (<math>\gamma</math>)
repuls(1,1) = 4.0 (<math>\lambda</math>)
Cmin(1,1,1) = 0.8 (<math>C_{\rm min}</math>)
augt1 = 1

Note that we label the atomic species of Au as 1. The variable <math>d = 0.05</math> is hard coded in '''meam_setup_done.F''' (when repuls < 5.0).

===MEAM Potential for Si===

We use the 'Si4' potential whose parameters are originally given in M. I. Baskes, Phys. Rev. B 46, 2727 (1992), and later modified by Ryu and Cai, J. Phys. Condens. Matter 22, 055401 (2010).

The main parameters in the MEAM potential is specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines correspond to 'Siz' is given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Si4' 'dia' 4. 14 28.086 4.87 4.4 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Si}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.431 4.63 1. 1.0 3.13 4.47 -1.8 1.48 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Si}</math> = '''rozero''' will be important only for cross-potential.

'''ibar''' is a setting used in the equation of state (EOS), and will be explained later.

The modification made in Ryu and Cai JPCM (2010) is specified in the '''AuSi2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Si==

The parameters for the cross potential are specified in '''AuSi2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below. The values correspond to Table 3 of Ryu and Cai, J. Phys. Condens. Matter, 22, 055401 (2010).

re(1,2) = 2.700 (<math>r_e</math>)
delta(1,2) = 0.125 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.819 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.26 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.95 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 1.85 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

Table 3 of Ryu and Cai (2010) gives <math>E_c ({\rm AuSi}) = 4.155</math>. This value is related to delta(1,2) through

<math>E_c ({\rm AuSi}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Si}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 4.63) - 0.125 = 4.155</math>.

<math>\rho_0^{\rm Si} / \rho_0^{\rm Au}</math> = 1.48 because of the <math>\rho_0^{\rm Si}</math> and <math>\rho_0^{\rm Au}</math> values specified above.

Cmax = 2.8 is the default value.

==Benchmark in MD++==

Compile the code using the following command.

make meam-lammps build=R SYS=gpp

Use the following command to compute the equilibrium lattice constant and cohesive energy of pure Au (FCC). You can download the [[media:si-au.tcl.txt | si-au.tcl]] from the link.

bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 1

The results are

a0 = 4.07300759775 Angstrom
Ecoh = -3.92996804082 eV

Use the following command to compute the equilibrium lattice constant and cohesive energy of pure Si (DC).

bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 0

The results are

a0 = 5.43100051581 Angstrom
Ecoh = -4.63000000205 eV

Use the following command to compute the equilibrium lattice constant and cohesive energy of Au-Si (B1).

bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 2

The results are

a0 = 5.4 Angstrom
Ecoh = -4.155000000083061 eV

===Impurity energy===

Use the following command to compute the impurity of a Au atom in Si DC lattice.

bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 4

The results depend slightly on the cell size
cell size, Eimp(eV)
3x3x3 3.914
4x4x4 3.968
5x5x5 3.987
10x10x10 4.005
20x20x20 4.008

The result in the paper (S. Ryu and W.Cai JPCM 22 055401 (2010), Table 2,
is <math>E_2 = 3.968</math> (eV) for a Au atom in Si DC crystal.
So it seems that the result in JPCM (2010) corresponds to the 4x4x4 cell here.

Use the following command to compute the impurity of a Si atom in Au fcc lattice.

bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 3

cell size, Eimp(eV)
2x2x2 0.639
3x3x3 0.660
4x4x4 0.665
5x5x5 0.667
10x10x10 0.669
20x20x20 0.669

The result in the paper (S. Ryu and W.Cai JPCM 22 055401 (2010), Table 2,
is <math>E_1 = 0.636</math> (eV) for a Si atom in Au FCC crystal.
So it seems that for a Si in Au FCC crystal, the predicted results here using
the 2x2x2 cell corresponds to the value in JPCM (2010).

Classical Simulation of GeAu droplet on Ge substrate

2016-12-01T12:03:05Z

Adrianos:

Classical Simulation of GeAu droplet on Ge substrate

2016-12-01T11:58:55Z

Adrianos: /* Pure element with impurities */

Classical Simulation of GeAu droplet on Ge substrate

2016-12-01T11:55:34Z

Adrianos:

Classical Simulation of GeAu droplet on Ge substrate

2016-12-01T11:47:31Z

Adrianos: Created page with " Molecular Dynamics simulations of Semiconductor Nanowires <DIV> Adri..."

Tutorial:Members Only

2016-12-01T11:44:15Z

Adrianos: /* Manuals for Group Members */

== Manuals for Group Members ==

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Scientific Articles
|-
| [https://micro.stanford.edu/journal-repository Journal Repository]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | ParaDiS
|-
| [[ParaDiS Cylinder Code Manuals ]]
|-
| [[ParaDiS ThinFilm Code Manuals]]
|-
| [[ParaDiS Aniso Code Manuals]]
|-
| [[ Cross-slip in ParaDiS]]
|-
| [[Parallel Cluster Guides]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | MD++
|-
| [[Foward Flux Sampling in MD++]]
|-
| [[Torsion and Bending PBC in MD++]]
|-
| [[A Polygonal Dislocation Loop in MD++]]
|-
| [[Use of Ewald Summation in MD++]]
|-
| [[MEAM Potential for Au-Si]]
|-
| [[MEAM Potential for Au-Ge]]
|-
| [[Computing Binary Phase Diagram in MD++]]
|-
| [[Classical Simulation of GeAu droplet on Ge substrate]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | LAMMPS
|-
| [[Use Au-Si MEAM Potential in LAMMPS]]
|-
| [[Compile LAMMPS on GPU on Sherlock]]
|-
| [[Perform Nanoindentation on Al-Mg Alloy]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Phase Field
|-
| [[Summary of Nanowire Growth Mechanism]]
|-
| [[Single Phase Field Model with Isotropic Surface Energy]]
|-
| [[Single Phase Field Model with Anisotropic Surface Energy]]
|-
| [[Multi Phase Field Model with Isotropic Interface Energy]]
|-
| [[Multi Phase Field Model with Anisotropic Interface Energy]]
|-
| [[Multi Phase Field Model (Revised Formulation)]]
|-
| [[Parallelization of the Phase Field Model]]
|-
| [[Phase Field Model for Grain Evolution]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | VASP
|-
| [[VASP Computing Bulk Modulus of Au]]
|-
| [[VASP Computing Bulk Modulus of ZrO2]]
|-
| [[VASP Computing Bulk Modulus of YSZ]]
|-
| [[VASP Computing Density of States of YSZ]]
|-
| [[VASP Computing Generalized Stacking Fault Energy of Au]]
|-
| [[VASP Computing Ideal Shear Strength of Au]]
|-
| [[VASP terminology]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Qbox
|-
| [[Qbox Computing Bulk Modulus of Au]]
|-
| [[Qbox Computing Bulk Modulus of ZrO2]]
|-
| [[Qbox Implemention of Magnetic Field]]
|-
| [[Qbox Generating Pseudopotentials]]
|-
| [[Ab Initio Simulations of Condensed Matter under Arbitrary Magnetic Field | MPBC/Qbox draft1]]
|-
| [[Predicting Molecular and Electronic Response to Magnetic Field from First Principles | MPBC/Qbox draft2]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | C++
|-
| [[BOOST Library]]
|-
| [[Install GCC]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | LaTeX
|-
| [[Install LaTeX from Scratch]]
|-
| [[Beamer Presentations]]
|-
| [[TikZ package]]
|-
| [[PGFPLOTS]]
|-
| [[Asymptote]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Tools
|-
| [[Atom Eye]]
|-
| [[Gnuplot]]
|-
| [[Computational XRD]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Computers
|-
| [[Micro Maintenance]]
|-
| [[Libraries in SU-AHPCRC]]
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{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Fatigue Literature Review
|-
| [[2D Dislocation Dynamics]]
|-
| [[3D Dislocation Dynamics]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Outreach
|-
| [[Simulating Solids in MD++]]
|-
| [[Videos of bucky balls in motion]]
|}

This is my test

2016-12-01T11:40:24Z

Adrianos:

Tutorial for MD simulations of semiconductor NW
(MD++,LAMMPS,MATLAB
<DIV>
Adriano Santana
</DIV>
 Created Dec, 2016


This tutorial discusses the procedure of creating, running and analyzing the data for semiconductor nanowire (NW) simulations, SiAu, GeAu etc. Here we will employ MD++ to create
the structures (solid plus liquid droplet), LAMMPS to run classical MD on a cluster and MATLAB to analyze (plot) histograms, velocity growth, growth etc.

===Pure element with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au FCC lattice with Si impurities and Si DC with gold impurities. First calculate the free energy of Au-fcc crystal with a Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

Simultaneously one can also calculate the free energy of Si-DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi binary alloy===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the third argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

===Plot binary phase diagram===

Finally, place in the same folder all the *.dat files from the previous simulations,
Au with Si impurity, Si with Au impurity and the AuSi files for for the binary alloy
with the range of compositions. you'll also need these three scripts:
plot_liquid_free_energy.m, comtan.m and polyfunc.m create

Launch MATLAB and run plot_liquid_free_energy.m and you should get
the binary phase diagram.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

This is my test

2016-12-01T11:35:14Z

Adrianos: Created page with " Tutorial for MD simulations of semiconductor NW (MD++,LAMMPS,MATLAB <DIV> <ST..."

Tutorial for MD simulations of semiconductor NW
(MD++,LAMMPS,MATLAB
<DIV>
Yanming Wang, Adriano Santana and Wei Cai
</DIV>
 Created Nov, 2015


This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.

===Pure element with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au FCC lattice with Si impurities and Si DC with gold impurities. First calculate the free energy of Au-fcc crystal with a Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

Simultaneously one can also calculate the free energy of Si-DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi binary alloy===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the third argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

===Plot binary phase diagram===

Finally, place in the same folder all the *.dat files from the previous simulations,
Au with Si impurity, Si with Au impurity and the AuSi files for for the binary alloy
with the range of compositions. you'll also need these three scripts:
plot_liquid_free_energy.m, comtan.m and polyfunc.m create

Launch MATLAB and run plot_liquid_free_energy.m and you should get
the binary phase diagram.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Tutorial:Members Only

2016-12-01T11:31:54Z

Adrianos: /* Manuals for Group Members */

== Manuals for Group Members ==

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Scientific Articles
|-
| [https://micro.stanford.edu/journal-repository Journal Repository]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | ParaDiS
|-
| [[ParaDiS Cylinder Code Manuals ]]
|-
| [[ParaDiS ThinFilm Code Manuals]]
|-
| [[ParaDiS Aniso Code Manuals]]
|-
| [[ Cross-slip in ParaDiS]]
|-
| [[Parallel Cluster Guides]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | MD++
|-
| [[Foward Flux Sampling in MD++]]
|-
| [[Torsion and Bending PBC in MD++]]
|-
| [[A Polygonal Dislocation Loop in MD++]]
|-
| [[Use of Ewald Summation in MD++]]
|-
| [[MEAM Potential for Au-Si]]
|-
| [[MEAM Potential for Au-Ge]]
|-
| [[Computing Binary Phase Diagram in MD++]]
|-
| [[this is my test]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | LAMMPS
|-
| [[Use Au-Si MEAM Potential in LAMMPS]]
|-
| [[Compile LAMMPS on GPU on Sherlock]]
|-
| [[Perform Nanoindentation on Al-Mg Alloy]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Phase Field
|-
| [[Summary of Nanowire Growth Mechanism]]
|-
| [[Single Phase Field Model with Isotropic Surface Energy]]
|-
| [[Single Phase Field Model with Anisotropic Surface Energy]]
|-
| [[Multi Phase Field Model with Isotropic Interface Energy]]
|-
| [[Multi Phase Field Model with Anisotropic Interface Energy]]
|-
| [[Multi Phase Field Model (Revised Formulation)]]
|-
| [[Parallelization of the Phase Field Model]]
|-
| [[Phase Field Model for Grain Evolution]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | VASP
|-
| [[VASP Computing Bulk Modulus of Au]]
|-
| [[VASP Computing Bulk Modulus of ZrO2]]
|-
| [[VASP Computing Bulk Modulus of YSZ]]
|-
| [[VASP Computing Density of States of YSZ]]
|-
| [[VASP Computing Generalized Stacking Fault Energy of Au]]
|-
| [[VASP Computing Ideal Shear Strength of Au]]
|-
| [[VASP terminology]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Qbox
|-
| [[Qbox Computing Bulk Modulus of Au]]
|-
| [[Qbox Computing Bulk Modulus of ZrO2]]
|-
| [[Qbox Implemention of Magnetic Field]]
|-
| [[Qbox Generating Pseudopotentials]]
|-
| [[Ab Initio Simulations of Condensed Matter under Arbitrary Magnetic Field | MPBC/Qbox draft1]]
|-
| [[Predicting Molecular and Electronic Response to Magnetic Field from First Principles | MPBC/Qbox draft2]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | C++
|-
| [[BOOST Library]]
|-
| [[Install GCC]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | LaTeX
|-
| [[Install LaTeX from Scratch]]
|-
| [[Beamer Presentations]]
|-
| [[TikZ package]]
|-
| [[PGFPLOTS]]
|-
| [[Asymptote]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Tools
|-
| [[Atom Eye]]
|-
| [[Gnuplot]]
|-
| [[Computational XRD]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Computers
|-
| [[Micro Maintenance]]
|-
| [[Libraries in SU-AHPCRC]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Fatigue Literature Review
|-
| [[2D Dislocation Dynamics]]
|-
| [[3D Dislocation Dynamics]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Outreach
|-
| [[Simulating Solids in MD++]]
|-
| [[Videos of bucky balls in motion]]
|}

MEAM Potential for Au-Ge

2016-02-27T09:31:34Z

Adrianos: /* Cross Potential between Au and Ge */

MEAM Potential for Au-Ge
<DIV>
Adriano Santana and Wei Cai
</DIV>
 Created Aug, 2015, Last modified Sep, 2015


This tutorial explains how to specify the parameters for the Au-Ge MEAM potential in MD++. It starts with the parameters in pure Au and pure Ge potentials, then talks about the Au-Ge cross potential.
<HR>

==Potential for Pure Elements==

===Original MEAM Potential for Au===

The details for the original 'Au' potential can be found here
JUST REFER TO OTHER PAGE....!

UNDER CONSTRUCTION!!!!!

===MEAM Potential for Ge===

We use the 'Ge5' potential whose parameters are originally given in M. I. Baskes,
The main parameters in the MEAM potential are specified in the '''meamf''' file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines corresponding to 'Ge5' are given below. Most of these parameters correspond to Table III of Baskes PRB (1992), as shown below.

<math>\alpha_i</math> <math>\beta_i^{(0)}</math> <math>\beta_i^{(1)}</math> <math>\beta_i^{(2)}</math> <math>\beta_i^{(3)}</math>
elt lat z ielement atwt alpha b0 b1 b2 b3
'Ge5' 'dia' 4. 32 72.64 4.98 4.55 5.5 5.5 5.5

<math>(R_i^0)</math> <math>E_i^0</math> <math>A_i</math> <math>t_i^{(0)}</math> <math>t_i^{(1)}</math> <math>t_i^{(2)}</math> <math>t_i^{(3)}</math> <math>\rho_0^{\rm Ge}</math>
alat esub asub t0 t1 t2 t3 rozero ibar
5.6575 3.85 1.0 1.0 4.02 5.23 -1.6 0.9858 0

Note that the nearest neighbor distance <math> R_i^0 </math> = '''alat''' <math>\times \sqrt{3}/4</math> for the diamond cubic structure.

<math>\rho_0^{\rm Ge}</math> = '''rozero''' will be important only for cross-potential. In our fitting it takes the value 0.9858 instead of the original one of 1.35 in Baskes paper.

'''ibar''' is a setting used in the equation of state (EOS). ibar selects the G(gamma) function in Eq (4) and (5) of the paper by BJ Lee, PRB 68, 144112 (2003).

While the functional form is quite different, the modulus is almost not affected by the choice of ibar.

The parameters for the cross potential are specified in the '''AuGe2nn.meam''' file. The variables in Eq.(A.1) of Ryu and Cai JPCM (2010) are given in the parenthesis.

erose_form = 3
rc = 4.5
attrac(2,2) = -0.36 (<math>\gamma</math>)
repuls(2,2) = 16.0 (<math>\lambda</math>)
Cmin(2,2,2) = 1.85 (<math>C_{\rm min}</math>)

Note that we label the atomic species of Si as 2.

==Cross Potential between Au and Ge==

The parameters for the cross potential are specified in '''AuGe2nn.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below.
They are calculated from VASP LDA/US.

Similar values are found in Table 3 of Ryu and Cai, J. Phys. Condens. Matter, 22, 055401 (2010).

re(1,2) = 2.6505 (<math>r_e</math>)
delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
lattce(1,2) = b1
alpha(1,2) = 5.346 (<math>\alpha</math>)
attrac(1,2) = 0.0
repuls(1,2) = 0.26 (<math>\gamma</math>)
Cmin(1,1,2) = 1.9 (<math>C_{\min}(1,1,2)</math>)
Cmin(1,2,1) = 0.95 (<math>C_{\min}(1,2,1)</math>)
Cmin(1,2,2) = 1.85 (<math>C_{\min}(1,2,2)</math>)
Cmin(2,2,1) = 1.0 (<math>C_{\min}(2,2,1)</math>)

The values for <math>E_c ({\rm AuGe}) = 4.722</math>.
This value is related to delta(1,2) through

<math>E_c ({\rm AuGe}) = 0.5*[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 * (3.93 + 3.85) - 0.071 = 3.819</math>.

<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 0.989 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
<math>E_2 = 1.180 </math> eV Au impurity in DC Ge (MEAM)

These values are to be compared with VASP predictions

<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

Computing Binary Phase Diagram in MD++

2015-12-08T11:34:11Z

Adrianos: /* Au-Si with impurities */

Binary Phase Diagram Construction
from Free Energy Calculation
<DIV>
Yanming Wang, Adriano Santana and Wei Cai
</DIV>
 Created Nov, 2015


This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.

===Pure element with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au FCC lattice with Si impurities and Si DC with gold impurities. First calculate the free energy of Au-fcc crystal with a Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

Simultaneously one can also calculate the free energy of Si-DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi binary alloy===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the third argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

===Plot binary phase diagram===

Finally, place in the same folder all the *.dat files from the previous simulations,
Au with Si impurity, Si with Au impurity and the AuSi files for for the binary alloy
with the range of compositions. you'll also need these three scripts:
plot_liquid_free_energy.m, comtan.m and polyfunc.m create

Launch MATLAB and run plot_liquid_free_energy.m and you should get
the binary phase diagram.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Computing Binary Phase Diagram in MD++

2015-12-08T11:32:33Z

Adrianos: /* Plot binary phase diagram */

Binary Phase Diagram Construction
from Free Energy Calculation
<DIV>
Yanming Wang, Adriano Santana and Wei Cai
</DIV>
 Created Nov, 2015


This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.

===Au-Si with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au with Si impurities and Si with gold impurities. First calculate the free energy
of Au fcc crystal with Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

Simultaneously one can also calculate the free energy of Si DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi binary alloy===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the third argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

===Plot binary phase diagram===

Finally, place in the same folder all the *.dat files from the previous simulations,
Au with Si impurity, Si with Au impurity and the AuSi files for for the binary alloy
with the range of compositions. you'll also need these three scripts:
plot_liquid_free_energy.m, comtan.m and polyfunc.m create

Launch MATLAB and run plot_liquid_free_energy.m and you should get
the binary phase diagram.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Computing Binary Phase Diagram in MD++

2015-12-08T11:23:35Z

Adrianos: /* AuSi binary alloy */

Binary Phase Diagram Construction
from Free Energy Calculation
<DIV>
Yanming Wang, Adriano Santana and Wei Cai
</DIV>
 Created Nov, 2015


This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.

===Au-Si with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au with Si impurities and Si with gold impurities. First calculate the free energy
of Au fcc crystal with Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

Simultaneously one can also calculate the free energy of Si DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi binary alloy===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the third argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

===Plot binary phase diagram===

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Computing Binary Phase Diagram in MD++

2015-12-08T11:22:50Z

Adrianos: /* AuSi liquidus mixture */

Binary Phase Diagram Construction
from Free Energy Calculation
<DIV>
Yanming Wang, Adriano Santana and Wei Cai
</DIV>
 Created Nov, 2015


This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.

===Au-Si with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au with Si impurities and Si with gold impurities. First calculate the free energy
of Au fcc crystal with Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

Simultaneously one can also calculate the free energy of Si DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi binary alloy===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the third argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Computing Binary Phase Diagram in MD++

2015-12-08T06:21:36Z

Adrianos: /* AuSi liquidus mixture */

Binary Phase Diagram Construction
from Free Energy Calculation
<DIV>
Yanming Wang, Adriano Santana and Wei Cai
</DIV>
 Created Nov, 2015


This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.

===Au-Si with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au with Si impurities and Si with gold impurities. First calculate the free energy
of Au fcc crystal with Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

Simultaneously one can also calculate the free energy of Si DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi liquidus mixture===

This tcl scripts, wcr_AuSi_Liquid.tcl,
calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the thitd argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Computing Binary Phase Diagram in MD++

2015-12-08T06:20:44Z

Adrianos: /* AuSi liquidus mixture */

Binary Phase Diagram Construction
from Free Energy Calculation
<DIV>
Yanming Wang, Adriano Santana and Wei Cai
</DIV>
 Created Nov, 2015


This tutorial discusses how to perform a series of simulations that generate free energy data of pure solid, solid with impurity and binary liquid alloy with different mixing ratio. Based on these data, the binary phase diagram can be obtained from common tangent construction using the free energy curves. As an example this tutorial explains how to produce the binary phase diagram for the Au-Si system.

===Au-Si with impurities===

The first script, wcrAuSi_Solid_imp.tcl, run MC simulations and produces the free energy raw data for Au with Si impurities and Si with gold impurities. First calculate the free energy
of Au fcc crystal with Si impurity:

<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Au1 1701 2.70
</pre>

The script takes four arguments, the first one ranges from 1-7.
the second is the number of repetitions. The third one is the label for the chemical
element: 'Au1', 'Si4', etc. which are all found inside the script. The fourth
argument is a division factor, 1701/2.70 equals 629 . Hence, the range of
temperatures will be from 1701 to 629 K.

Simultaneously one can also calculate the free energy of Si DC crystal with a gold impurity as:
<pre>
meam-lammps_gpp wcrAuSi_Solid_imp.tcl 1 1 Si4 1701 2.70
</pre>

After the two scripts finish four MATLAB scripts are produced in the Binary_AuSi_3 folder:

===AuSi liquidus mixture===

This tcl scripts calculates the data needed for the binary system mixture:

<pre>
meam-lammps_intel scripts/work/si_au/wcr_AuSi_Liquid.tcl 1 1 0 1701 2.704
</pre>

where the thitd argument from the left represents the silicon fraction in the
mixture, in this example 0%. The other arguments have similar meaning as above.

'''Step3'''

<pre>
results1
results2
</pre>

 '''to highlitght sth'''

Computing Binary Phase Diagram in MD++

2015-12-08T06:05:03Z

Adrianos: /* Au-Si with impurities */