1
2#
3# Help-file automatically created by helpdoc utility
4#
5#    !!! DO NOT EDIT: CHANGES WILL BE LOST !!!
6#
7
8
9# ------------------------------------------------------------------------
10help string_method -helpfmt helpdoc -helptext {
11      <ul>
12<li> <em>Variable: </em><big><b>string_method</b></big>
13</li>
14<br><li> <em>Type: </em>CHARACTER</li>
15<br><li> <em>Default: </em> 'neb'
16               </li>
17<br><li> <em>Description:</em>
18</li>
19<blockquote>
20<pre>
21A string describing the task to be performed. Options are:
22                  </pre>
23<dl style="margin-left: 1.5em;">
24<dt><tt><b>'neb'</b> :</tt></dt>
25<dd><pre style="margin-top: 0em; margin-bottom: -1em;"> nudget-elastic-band
26                  </pre></dd>
27</dl>
28<dl style="margin-left: 1.5em;">
29<dt><tt><b>'smd'</b> :</tt></dt>
30<dd><pre style="margin-top: 0em; margin-bottom: -1em;"> string-method-dynamics
31                  </pre></dd>
32</dl>
33</blockquote>
34</ul>
35
36}
37
38
39# ------------------------------------------------------------------------
40help restart_mode -helpfmt helpdoc -helptext {
41      <ul>
42<li> <em>Variable: </em><big><b>restart_mode</b></big>
43</li>
44<br><li> <em>Type: </em>CHARACTER</li>
45<br><li> <em>Default: </em> 'from_scratch'
46               </li>
47<br><li> <em>Description:</em>
48</li>
49<blockquote>
50<pre> Options are:
51                  </pre>
52<dl style="margin-left: 1.5em;">
53<dt><tt><b>'from_scratch'</b> :</tt></dt>
54<dd><pre style="margin-top: 0em; margin-bottom: -1em;"> from scratch
55                  </pre></dd>
56</dl>
57<dl style="margin-left: 1.5em;">
58<dt><tt><b>'restart'</b> :</tt></dt>
59<dd><pre style="margin-top: 0em; margin-bottom: -1em;"> from previous interrupted run
60                  </pre></dd>
61</dl>
62</blockquote>
63</ul>
64
65}
66
67
68# ------------------------------------------------------------------------
69help nstep_path -helpfmt helpdoc -helptext {
70      <ul>
71<li> <em>Variable: </em><big><b>nstep_path</b></big>
72</li>
73<br><li> <em>Type: </em>INTEGER</li>
74<br><li> <em>Default: </em>
751
76               </li>
77<br><li> <em>Description:</em>
78</li>
79<blockquote><pre>
80number of ionic + electronic steps
81               </pre></blockquote>
82</ul>
83
84}
85
86
87# ------------------------------------------------------------------------
88help num_of_images -helpfmt helpdoc -helptext {
89      <ul>
90<li> <em>Variable: </em><big><b>num_of_images</b></big>
91</li>
92<br><li> <em>Type: </em>INTEGER</li>
93<br><li> <em>Default: </em> 0
94               </li>
95<br><li> <em>Description:</em>
96</li>
97<blockquote><pre>
98Number of points used to discretize the path
99(it must be larger than 3).
100               </pre></blockquote>
101</ul>
102
103}
104
105
106# ------------------------------------------------------------------------
107help opt_scheme -helpfmt helpdoc -helptext {
108      <ul>
109<li> <em>Variable: </em><big><b>opt_scheme</b></big>
110</li>
111<br><li> <em>Type: </em>CHARACTER</li>
112<br><li> <em>Default: </em> 'quick-min'
113               </li>
114<br><li> <em>Description:</em>
115</li>
116<blockquote>
117<pre>
118Specify the type of optimization scheme:
119                  </pre>
120<dl style="margin-left: 1.5em;">
121<dt><tt><b>'sd'</b> :</tt></dt>
122<dd><pre style="margin-top: 0em; margin-bottom: -1em;">
123steepest descent
124                  </pre></dd>
125</dl>
126<dl style="margin-left: 1.5em;">
127<dt><tt><b>'broyden'</b> :</tt></dt>
128<dd><pre style="margin-top: 0em; margin-bottom: -1em;">
129quasi-Newton Broyden's second method (suggested)
130                  </pre></dd>
131</dl>
132<dl style="margin-left: 1.5em;">
133<dt><tt><b>'broyden2'</b> :</tt></dt>
134<dd><pre style="margin-top: 0em; margin-bottom: -1em;">
135another variant of the quasi-Newton Broyden's
136second method to be tested and compared with the
137previous one.
138                  </pre></dd>
139</dl>
140<dl style="margin-left: 1.5em;">
141<dt><tt><b>'quick-min'</b> :</tt></dt>
142<dd><pre style="margin-top: 0em; margin-bottom: -1em;">
143an optimisation algorithm based on the
144projected velocity Verlet scheme
145                  </pre></dd>
146</dl>
147<dl style="margin-left: 1.5em;">
148<dt><tt><b>'langevin'</b> :</tt></dt>
149<dd><pre style="margin-top: 0em; margin-bottom: -1em;">
150finite temperature langevin dynamics of the
151string (smd only). It is used to compute the
152average path and the free-energy profile.
153                  </pre></dd>
154</dl>
155</blockquote>
156</ul>
157
158}
159
160
161# ------------------------------------------------------------------------
162help CI_scheme -helpfmt helpdoc -helptext {
163      <ul>
164<li> <em>Variable: </em><big><b>CI_scheme</b></big>
165</li>
166<br><li> <em>Type: </em>CHARACTER</li>
167<br><li> <em>Default: </em> 'no-CI'
168               </li>
169<br><li> <em>Description:</em>
170</li>
171<blockquote>
172<pre>
173Specify the type of Climbing Image scheme:
174                  </pre>
175<dl style="margin-left: 1.5em;">
176<dt><tt><b>'no-CI'</b> :</tt></dt>
177<dd><pre style="margin-top: 0em; margin-bottom: -1em;">
178climbing image is not used
179                  </pre></dd>
180</dl>
181<dl style="margin-left: 1.5em;">
182<dt><tt><b>'auto'</b> :</tt></dt>
183<dd><pre style="margin-top: 0em; margin-bottom: -1em;">
184original CI scheme. The image highest in energy
185does not feel the effect of springs and is
186allowed to climb along the path
187                  </pre></dd>
188</dl>
189<dl style="margin-left: 1.5em;">
190<dt><tt><b>'manual'</b> :</tt></dt>
191<dd><pre style="margin-top: 0em; margin-bottom: -1em;">
192images that have to climb are manually selected.
193See also "CLIMBING_IMAGES" card
194                  </pre></dd>
195</dl>
196</blockquote>
197</ul>
198
199}
200
201
202# ------------------------------------------------------------------------
203help first_last_opt -helpfmt helpdoc -helptext {
204      <ul>
205<li> <em>Variable: </em><big><b>first_last_opt</b></big>
206</li>
207<br><li> <em>Type: </em>LOGICAL</li>
208<br><li> <em>Default: </em> .FALSE.
209               </li>
210<br><li> <em>Description:</em>
211</li>
212<blockquote><pre>
213Also the first and the last configurations are optimized
214"on the fly" (these images do not feel the effect of the springs).
215               </pre></blockquote>
216</ul>
217
218}
219
220
221# ------------------------------------------------------------------------
222help minimum_image -helpfmt helpdoc -helptext {
223      <ul>
224<li> <em>Variable: </em><big><b>minimum_image</b></big>
225</li>
226<br><li> <em>Type: </em>LOGICAL</li>
227<br><li> <em>Default: </em> .FALSE.
228               </li>
229<br><li> <em>Description:</em>
230</li>
231<blockquote><pre>
232Assume a "minimum image criterion" to build the path. If an atom
233moves by more than half the length of a crystal axis between one
234image and the next in the input (before interpolation),
235an appropriate periodic replica of that atom is chosen.
236Useful to avoid jumps in the initial reaction path.
237               </pre></blockquote>
238</ul>
239
240}
241
242
243# ------------------------------------------------------------------------
244help temp_req -helpfmt helpdoc -helptext {
245      <ul>
246<li> <em>Variable: </em><big><b>temp_req</b></big>
247</li>
248<br><li> <em>Type: </em>REAL</li>
249<br><li> <em>Default: </em> 0.D0 Kelvin
250               </li>
251<br><li> <em>Description:</em>
252</li>
253<blockquote><pre>
254Temperature used for the langevin dynamics of the string.
255               </pre></blockquote>
256</ul>
257
258}
259
260
261# ------------------------------------------------------------------------
262help ds -helpfmt helpdoc -helptext {
263      <ul>
264<li> <em>Variable: </em><big><b>ds</b></big>
265</li>
266<br><li> <em>Type: </em>REAL</li>
267<br><li> <em>Default: </em> 1.D0
268               </li>
269<br><li> <em>Description:</em>
270</li>
271<blockquote><pre>
272Optimisation step length ( Hartree atomic units ).
273If "opt_scheme"=="broyden", ds is used as a guess for the
274diagonal part of the Jacobian matrix.
275               </pre></blockquote>
276</ul>
277
278}
279
280
281# ------------------------------------------------------------------------
282grouphelp {k_max k_min} -helpfmt helpdoc -helptext {
283    <ul>
284<li> <em>Variables: </em><big><b>k_max, k_min</b></big>
285</li>
286<br><li> <em>Type: </em>REAL</li>
287<br><li> <em>Default: </em> 0.1D0 Hartree atomic units
288               </li>
289<br><li> <em>Description:</em>
290</li>
291<blockquote><pre>
292Set them to use a Variable Elastic Constants scheme
293elastic constants are in the range [ k_min, k_max ]
294this is useful to rise the resolution around the saddle point.
295               </pre></blockquote>
296</ul>
297
298}
299
300
301# ------------------------------------------------------------------------
302help path_thr -helpfmt helpdoc -helptext {
303      <ul>
304<li> <em>Variable: </em><big><b>path_thr</b></big>
305</li>
306<br><li> <em>Type: </em>REAL</li>
307<br><li> <em>Default: </em> 0.05D0 eV / Angstrom
308               </li>
309<br><li> <em>Description:</em>
310</li>
311<blockquote><pre>
312The simulation stops when the error ( the norm of the force
313orthogonal to the path in eV/A ) is less than path_thr.
314               </pre></blockquote>
315</ul>
316
317}
318
319
320# ------------------------------------------------------------------------
321help use_masses -helpfmt helpdoc -helptext {
322      <ul>
323<li> <em>Variable: </em><big><b>use_masses</b></big>
324</li>
325<br><li> <em>Type: </em>LOGICAL</li>
326<br><li> <em>Default: </em> .FALSE.
327               </li>
328<br><li> <em>Description:</em>
329</li>
330<blockquote><pre>
331If. TRUE. the optimisation of the path is performed using
332mass-weighted coordinates. Useful together with quick-min
333optimization scheme, if some bonds are much stiffer than
334others. By assigning a larger (fictitious) mass to atoms
335with stiff bonds, one may use a longer time step "ds"
336               </pre></blockquote>
337</ul>
338
339}
340
341
342# ------------------------------------------------------------------------
343help use_freezing -helpfmt helpdoc -helptext {
344      <ul>
345<li> <em>Variable: </em><big><b>use_freezing</b></big>
346</li>
347<br><li> <em>Type: </em>LOGICAL</li>
348<br><li> <em>Default: </em> .FALSE.
349               </li>
350<br><li> <em>Description:</em>
351</li>
352<blockquote><pre>
353If. TRUE. the images are optimised according to their error:
354only those images with an error larger than half of the largest
355are optimised. The other images are kept frozen.
356               </pre></blockquote>
357</ul>
358
359}
360
361
362# ------------------------------------------------------------------------
363help lfcpopt -helpfmt helpdoc -helptext {
364      <ul>
365<li> <em>Variable: </em><big><b>lfcpopt</b></big>
366</li>
367<br><li> <em>Type: </em>LOGICAL</li>
368<br><li> <em>Default: </em> .FALSE.
369               </li>
370<br><li> <em>See: </em> fcp_mu
371               </li>
372<br><li> <em>Description:</em>
373</li>
374<blockquote><pre>
375If .TRUE. perform a constant bias potential (constant-mu)
376calculation with ESM method (assume_isolated = 'esm' and
377esm_bc = 'bc2' or 'bc3' must be set in SYSTEM namelist).
378"fcp_mu" gives the target Fermi energy.
379See the header of PW/src/fcp.f90 for documentation
380               </pre></blockquote>
381</ul>
382
383}
384
385
386# ------------------------------------------------------------------------
387help fcp_mu -helpfmt helpdoc -helptext {
388      <ul>
389<li> <em>Variable: </em><big><b>fcp_mu</b></big>
390</li>
391<br><li> <em>Type: </em>REAL</li>
392<br><li> <em>Default: </em> 0.d0
393               </li>
394<br><li> <em>See: </em> lfcpopt
395               </li>
396<br><li> <em>Description:</em>
397</li>
398<blockquote><pre>
399If "lfcpopt" == .TRUE., gives the target Fermi energy [Ry].
400One can specify the total charge of the system for the first
401and last image by giving "fcp_tot_charge_first" and "fcp_tot_charge_last"
402so that the Fermi energy of these systems will be the target value,
403otherwise "first_last_opt" should be .TRUE.
404               </pre></blockquote>
405</ul>
406
407}
408
409
410# ------------------------------------------------------------------------
411help fcp_tot_charge_first -helpfmt helpdoc -helptext {
412      <ul>
413<li> <em>Variable: </em><big><b>fcp_tot_charge_first</b></big>
414</li>
415<br><li> <em>Type: </em>REAL</li>
416<br><li> <em>Default: </em> 0.d0
417               </li>
418<br><li> <em>See: </em> lfcpopt
419               </li>
420<br><li> <em>Description:</em>
421</li>
422<blockquote><pre>
423Total charge of the system ('tot_charge') for the first image.
424Initial 'tot_charge' for intermediate images will be given by
425linear interpolation of "fcp_tot_charge_first" and "fcp_tot_charge_last"
426               </pre></blockquote>
427</ul>
428
429}
430
431
432# ------------------------------------------------------------------------
433help fcp_tot_charge_last -helpfmt helpdoc -helptext {
434      <ul>
435<li> <em>Variable: </em><big><b>fcp_tot_charge_last</b></big>
436</li>
437<br><li> <em>Type: </em>REAL</li>
438<br><li> <em>Default: </em> 0.d0
439               </li>
440<br><li> <em>See: </em> lfcpopt
441               </li>
442<br><li> <em>Description:</em>
443</li>
444<blockquote><pre>
445Total charge of the system ('tot_charge') for the last image.
446Initial 'tot_charge' for intermediate images will be given by
447linear interpolation of "fcp_tot_charge_first" and "fcp_tot_charge_last"
448               </pre></blockquote>
449</ul>
450
451}
452
453
454# ------------------------------------------------------------------------
455help climbing_images_list -helpfmt helpdoc -helptext {
456    <ul>
457<li> <em>Variables: </em><big><b> index1, index2, ... indexN
458                  </b></big>
459</li>
460<br><li> <em>Type: </em>INTEGER</li>
461<br><li> <em>Description:</em>
462</li>
463<blockquote><pre>
464index1, index2, ..., indexN are indices of the images to which the
465Climbing-Image procedure apply. If more than one image is specified
466they must be separated by a comma.
467                  </pre></blockquote>
468</ul>
469
470}
471
472