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38 /* This file is completely threadsafe - keep it that way! */
39 #include "gmxpre.h"
40
41 #include "hackblock.h"
42
43 #include <cstring>
44
45 #include "gromacs/gmxpreprocess/notset.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/mdtypes/md_enums.h"
48 #include "gromacs/topology/atoms.h"
49 #include "gromacs/topology/symtab.h"
50 #include "gromacs/utility/arrayref.h"
51 #include "gromacs/utility/cstringutil.h"
52 #include "gromacs/utility/exceptions.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/gmxassert.h"
55 #include "gromacs/utility/smalloc.h"
56 #include "gromacs/utility/stringcompare.h"
57
58 /* these MUST correspond to the enum in hackblock.h */
59 const char* btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };
60 const int btsNiatoms[ebtsNR] = { 2, 3, 4, 4, 2, 5 };
61
type() const62 MoleculePatchType MoleculePatch::type() const
63 {
64 if (oname.empty() && !nname.empty())
65 {
66 return MoleculePatchType::Add;
67 }
68 else if (!oname.empty() && nname.empty())
69 {
70 return MoleculePatchType::Delete;
71 }
72 else if (!oname.empty() && !nname.empty())
73 {
74 return MoleculePatchType::Replace;
75 }
76 else
77 {
78 GMX_THROW(gmx::InvalidInputError("Unknown type of atom modification"));
79 }
80 }
81
clearModificationBlock(MoleculePatchDatabase * globalPatches)82 void clearModificationBlock(MoleculePatchDatabase* globalPatches)
83 {
84 globalPatches->name.clear();
85 globalPatches->hack.clear();
86 for (int i = 0; i < ebtsNR; i++)
87 {
88 globalPatches->rb[i].b.clear();
89 }
90 }
91
92 #define safe_strdup(str) (((str) != NULL) ? gmx_strdup(str) : NULL)
93
contains_char(const BondedInteraction & s,char c)94 static bool contains_char(const BondedInteraction& s, char c)
95 {
96
97 bool bRet = false;
98 for (int i = 0; i < MAXATOMLIST; i++)
99 {
100 if (!s.a[i].empty() && s.a[i][0] == c)
101 {
102 bRet = true;
103 }
104 }
105
106 return bRet;
107 }
108
rbonded_find_atoms_in_list(const BondedInteraction & b,gmx::ArrayRef<const BondedInteraction> blist,int natoms)109 static int rbonded_find_atoms_in_list(const BondedInteraction& b,
110 gmx::ArrayRef<const BondedInteraction> blist,
111 int natoms)
112 {
113 int foundPos = -1;
114
115 for (auto it = blist.begin(); (it != blist.end()) && (foundPos < 0); it++)
116 {
117 bool atomsMatch = true;
118 for (int k = 0; k < natoms && atomsMatch; k++)
119 {
120 atomsMatch = atomsMatch && (b.a[k] == it->a[k]);
121 }
122 /* Try reverse if forward match did not work */
123 if (!atomsMatch)
124 {
125 atomsMatch = true;
126 for (int k = 0; k < natoms && atomsMatch; k++)
127 {
128 atomsMatch = atomsMatch && (b.a[k] == it->a[natoms - 1 - k]);
129 }
130 }
131 if (atomsMatch)
132 {
133 foundPos = std::distance(blist.begin(), it);
134 /* If all the atoms AND all the parameters match, it is likely that
135 * the user made a copy-and-paste mistake (since it would be much cheaper
136 * to just bump the force constant 2x if you really want it twice).
137 * Since we only have the unparsed string here we can only detect
138 * EXACT matches (including identical whitespace).
139 */
140 if (b.s == it->s)
141 {
142 gmx_warning("Duplicate line found in or between hackblock and rtp entries");
143 }
144 }
145 }
146 return foundPos;
147 }
148
mergeBondedInteractionList(gmx::ArrayRef<const BondedInteractionList> s,gmx::ArrayRef<BondedInteractionList> d,bool bMin,bool bPlus)149 bool mergeBondedInteractionList(gmx::ArrayRef<const BondedInteractionList> s,
150 gmx::ArrayRef<BondedInteractionList> d,
151 bool bMin,
152 bool bPlus)
153 {
154 bool bBondsRemoved = false;
155 for (int i = 0; i < ebtsNR; i++)
156 {
157 if (!s[i].b.empty())
158 {
159 /* Record how many bonds we have in the destination when we start.
160 *
161 * If an entry is present in the hackblock (destination), we will
162 * not add the one from the main rtp, since the point is for hackblocks
163 * to overwrite it. However, if there is no hackblock entry we do
164 * allow multiple main rtp entries since some forcefield insist on that.
165 *
166 * We accomplish this by checking the position we find an entry in,
167 * rather than merely checking whether it exists at all.
168 * If that index is larger than the original (hackblock) destination
169 * size, it was added from the main rtp, and then we will allow more
170 * such entries. In contrast, if the entry found has a lower index
171 * it is a hackblock entry meant to override the main rtp, and then
172 * we don't add the main rtp one.
173 */
174 int nbHackblockStart = d[i].b.size();
175
176 for (const auto& b : s[i].b)
177 {
178 /* Check if this bonded string already exists before adding.
179 * We are merging from the main RTP to the hackblocks, so this
180 * will mean the hackblocks overwrite the man RTP, as intended.
181 */
182 int index = rbonded_find_atoms_in_list(b, d[i].b, btsNiatoms[i]);
183 /* - If we did not find this interaction at all, the index will be -1,
184 * and then we should definitely add it to the merged hackblock and rtp.
185 *
186 * Alternatively, if it was found, index will be >=0.
187 * - In case this index is lower than the original number of entries,
188 * it is already present as a *hackblock* entry, and those should
189 * always override whatever we have listed in the RTP. Thus, we
190 * should just keep that one and not add anything from the RTP.
191 * - Finally, if it was found, but with an index higher than
192 * the original number of entries, it comes from the RTP rather
193 * than hackblock, and then we must have added it ourselves
194 * in a previous iteration. In that case it is a matter of
195 * several entries for the same sequence of atoms, and we allow
196 * that in the RTP. In this case we should simply copy all of
197 * them, including this one.
198 */
199 if (index < 0 || index >= nbHackblockStart)
200 {
201 if (!(bMin && contains_char(b, '-')) && !(bPlus && contains_char(b, '+')))
202 {
203 d[i].b.push_back(b);
204 }
205 else if (i == ebtsBONDS)
206 {
207 bBondsRemoved = true;
208 }
209 }
210 else
211 {
212 /* This is the common case where a hackblock entry simply
213 * overrides the RTP, so we cannot warn here.
214 */
215 }
216 }
217 }
218 }
219 return bBondsRemoved;
220 }
221
copyPreprocessResidues(const PreprocessResidue & s,PreprocessResidue * d,t_symtab * symtab)222 void copyPreprocessResidues(const PreprocessResidue& s, PreprocessResidue* d, t_symtab* symtab)
223 {
224 *d = s;
225 d->atom.clear();
226 for (const auto& a : s.atom)
227 {
228 d->atom.push_back(a);
229 }
230 d->atomname.clear();
231 for (const auto& a : s.atomname)
232 {
233 d->atomname.push_back(put_symtab(symtab, *a));
234 }
235 d->cgnr.clear();
236 for (const auto& c : s.cgnr)
237 {
238 d->cgnr.push_back(c);
239 }
240 for (int i = 0; i < ebtsNR; i++)
241 {
242 d->rb[i].type = s.rb[i].type;
243 d->rb[i].b.clear();
244 }
245 mergeBondedInteractionList(s.rb, d->rb, FALSE, FALSE);
246 }
247
mergeAtomModifications(const MoleculePatchDatabase & s,MoleculePatchDatabase * d)248 void mergeAtomModifications(const MoleculePatchDatabase& s, MoleculePatchDatabase* d)
249 {
250 for (const auto& h : s.hack)
251 {
252 d->hack.push_back(h);
253 }
254 }
255
mergeAtomAndBondModifications(const MoleculePatchDatabase & s,MoleculePatchDatabase * d)256 void mergeAtomAndBondModifications(const MoleculePatchDatabase& s, MoleculePatchDatabase* d)
257 {
258 mergeAtomModifications(s, d);
259 mergeBondedInteractionList(s.rb, d->rb, FALSE, FALSE);
260 }
261
copyModificationBlocks(const MoleculePatchDatabase & s,MoleculePatchDatabase * d)262 void copyModificationBlocks(const MoleculePatchDatabase& s, MoleculePatchDatabase* d)
263 {
264 *d = s;
265 d->name = s.name;
266 d->hack.clear();
267 for (int i = 0; i < ebtsNR; i++)
268 {
269 d->rb[i].b.clear();
270 }
271 mergeAtomAndBondModifications(s, d);
272 }
273
274 #undef safe_strdup
275