This file is indexed.

/usr/share/octave/packages/secs2d-0.0.8/ThDDGOX/ThDDGOXnlpoisson.m is in octave-secs2d 0.0.8-5.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
function [V,n,p,res,niter] = ThDDGOXnlpoisson (mesh,Dsides,Sinodes,SiDnodes,...
                                               Sielements,Vin,Vthn,Vthp,...
					       nin,pin,...
                                               Fnin,Fpin,D,l2,l2ox,...
                                               toll,maxit,verbose)

  %%  
  %%   [V,n,p,res,niter] = DDGOXnlpoisson (mesh,Dsides,Sinodes,Vin,nin,pin,...
  %%                                       Fnin,Fpin,D,l2,l2ox,toll,maxit,verbose)
  %%
  %%  solves $$ -\lambda^2 V'' + (n(V,Fn,Tn) - p(V,Fp,Tp) -D) = 0$$
  %%


  %% This file is part of 
  %%
  %%            SECS2D - A 2-D Drift--Diffusion Semiconductor Device Simulator
  %%         -------------------------------------------------------------------
  %%            Copyright (C) 2004-2006  Carlo de Falco
  %%
  %%
  %%
  %%  SECS2D is free software; you can redistribute it and/or modify
  %%  it under the terms of the GNU General Public License as published by
  %%  the Free Software Foundation; either version 2 of the License, or
  %%  (at your option) any later version.
  %%
  %%  SECS2D is distributed in the hope that it will be useful,
  %%  but WITHOUT ANY WARRANTY; without even the implied warranty of
  %%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  %%  GNU General Public License for more details.
  %%
  %%  You should have received a copy of the GNU General Public License
  %%  along with SECS2D; If not, see <http://www.gnu.org/licenses/>.

	global DDGOXNLPOISSON_LAP DDGOXNLPOISSON_MASS DDGOXNLPOISSON_RHS 

	%% Set some useful constants
	dampit 		= 3;
	dampcoeff	= 2;


	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	%% setup FEM data structures
	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

	nodes=mesh.p;
	elements=mesh.t;
	Nnodes = length(nodes);
	Nelements = length(elements);

	% Set list of nodes with Dirichelet BCs
	Dnodes = Unodesonside(mesh,Dsides);

	% Set values of Dirichelet BCs
	Bc     = zeros(length(Dnodes),1);
	% Set list of nodes without Dirichelet BCs
	Varnodes = setdiff([1:Nnodes],Dnodes);


	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	%%
	%% 		initialization:
	%% 		we're going to solve
	%% 		$$ - \lambda^2 (\delta V)'' 
	%%                              + (\frac{\partial n}{\partial V} 
	%%                              - \frac{\partial p}{\partial V})= -R $$
	%%
	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

	%% set $$ n_1 = nin $$ and $$ V = Vin $$
	V = Vin;
	Fn = Fnin;
	Fp = Fpin;
	n = exp((V(Sinodes)-Fn)./Vthn);
	p = exp((-V(Sinodes)+Fp)./Vthp);
	n(SiDnodes) = nin(SiDnodes);
	p(SiDnodes) = pin(SiDnodes);


	%%%
	%%% Compute LHS matrices
	%%%

	%% let's compute  FEM approximation of $$ L = -  \frac{d^2}{x^2} $$
	if (isempty(DDGOXNLPOISSON_LAP))
	  coeff = l2ox * ones(Nelements,1);
	  coeff(Sielements)=l2;
	  DDGOXNLPOISSON_LAP = Ucomplap (mesh,coeff);
	end

	%% compute $$ Mv = ( n + p)  $$
	%% and the (lumped) mass matrix M
	if (isempty(DDGOXNLPOISSON_MASS))
	  coeffe = zeros(Nelements,1);
	  coeffe(Sielements)=1;
	  DDGOXNLPOISSON_MASS = Ucompmass2(mesh,ones(Nnodes,1),coeffe);
	end
	freecarr=zeros(Nnodes,1);
	freecarr(Sinodes)=(n./Vthn + p./Vthp);
	Mv      =  freecarr;
	M       =  DDGOXNLPOISSON_MASS*spdiag(Mv);

	%%%
	%%% Compute RHS vector (-residual)
	%%%

	%% now compute $$ T0 = \frac{q}{\epsilon} (n - p - D) $$
	if (isempty(DDGOXNLPOISSON_RHS))
	  coeffe = zeros(Nelements,1);
	  coeffe(Sielements)=1;
	  DDGOXNLPOISSON_RHS = Ucompconst (mesh,ones(Nnodes,1),coeffe);
	end
	totcharge = zeros(Nnodes,1);
	totcharge(Sinodes)=(n - p - D);
	Tv0   = totcharge;
	T0    = Tv0 .* DDGOXNLPOISSON_RHS;

	%% now we're ready to build LHS matrix and RHS of the linear system for 1st Newton step
	  A 		= DDGOXNLPOISSON_LAP + M;
	  R 		= DDGOXNLPOISSON_LAP * V  + T0; 

	  %% Apply boundary conditions
	  A (Dnodes,:) = [];
	  A (:,Dnodes) = [];
	  R(Dnodes)  = [];

	  %% we need $$ \norm{R_1} $$ and $$ \norm{R_k} $$ for the convergence test   
	    normr(1)	=  norm(R,inf);
	    relresnorm 	= 1;
	    reldVnorm   = 1;
	    normrnew	= normr(1);
	    dV          = V*0;

	    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	    %%
	    %% START OF THE NEWTON CYCLE
	    %%
	    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
	    for newtit=1:maxit
	      if (verbose>2)
		fprintf(1,'\n***\nNewton iteration: %d, reldVnorm = %e\n***\n',newtit,reldVnorm);
	      end

	      %  A(1,end)=realmin;
	    dV(Varnodes) =(A)\(-R);
	    dV(Dnodes)=0;
	    
	    
	    %%%%%%%%%%%%%%%%%%
	    %% Start of th damping procedure
	    %%%%%%%%%%%%%%%%%%
	    tk = 1;
	    for dit = 1:dampit
	      if (verbose>2)
		fprintf(1,'\ndamping iteration: %d, residual norm = %e\n',dit,normrnew);
	      end
	      Vnew   = V + tk * dV;
	      
	      n = exp((Vnew(Sinodes)-Fn)./Vthn);
	      p = exp((-Vnew(Sinodes)+Fp)./Vthp);
	      n(SiDnodes) = nin(SiDnodes);
	      p(SiDnodes) = pin(SiDnodes);
	      
	      
	      %%%
	      %%% Compute LHS matrices
	      %%%
	      
	      %% let's compute  FEM approximation of $$ L = -  \frac{d^2}{x^2} $$
	      %L      = Ucomplap (mesh,ones(Nelements,1));
	      
	      %% compute $$ Mv =  ( n + p)  $$
	      %% and the (lumped) mass matrix M
	      freecarr=zeros(Nnodes,1);
	      freecarr(Sinodes)=(n./Vthn + p./Vthp);  
	      Mv   =  freecarr;
	      M    =  DDGOXNLPOISSON_MASS*spdiag(Mv);
	      
	      %%%
	      %%% Compute RHS vector (-residual)
	      %%%
	      
	      %% now compute $$ T0 = \frac{q}{\epsilon} (n - p - D) $$
	      totcharge( Sinodes)=(n - p - D);
	      Tv0   = totcharge;
	      T0    = Tv0 .* DDGOXNLPOISSON_RHS;%T0    = Ucompconst (mesh,Tv0,ones(Nelements,1));
	      
	      %% now we're ready to build LHS matrix and RHS of the linear system for 1st Newton step
		A 		= DDGOXNLPOISSON_LAP + M;
		R 		= DDGOXNLPOISSON_LAP * Vnew  + T0; 
		
		%% Apply boundary conditions
		A (Dnodes,:) = [];
		A (:,Dnodes) = [];
		R(Dnodes)  = [];
		
		%% compute $$ | R_{k+1} | $$ for the convergence test
		  normrnew= norm(R,inf);
		  
		  % check if more damping is needed
		    if (normrnew > normr(newtit))
		      tk = tk/dampcoeff;
		    else
		      if (verbose>2)
			fprintf(1,'\nexiting damping cycle because residual norm = %e \n-----------\n',normrnew);
		      end		
		      break
		    end	
		  end
		  
		  V		            = Vnew;	
		  normr(newtit+1) 	= normrnew;
		  dVnorm              = norm(tk*dV,inf);
		  pause(.1);
		  % check if convergence has been reached
		    reldVnorm           = dVnorm / norm(V,inf);
		    if (reldVnorm <= toll)
		      if(verbose>2)
			fprintf(1,'\nexiting newton cycle because reldVnorm= %e \n',reldVnorm);
		      end
		      break
		    end

		  end

		  res = normr;
		  niter = newtit;